Mr Obama delivered the message as he met leaders of the Asean grouping of south-east Asian nations in Singapore.
White House press secretary said Mr Obama raised the issue "directly" with General Thein Sein.
Ms Suu Kyi's house arrest was extended in August beyond the elections planned for next year. She has spent 14 years in detention in the past two decades.
Lawyers for Ms Suu Kyi, a Nobel peace prize laureate, have lodged an appeal with the Supreme Court against her extended house arrest.
The Apec summit brings together leaders of the 10-member Association of South East Asian Nations (Asean), which includes Burma.
Before the closed talks in a hotel room, Mr Obama and the Asean leaders stood in a line on a stage, crossing their arms to shake hands with the leader on either side.
Gen Thein Sein was not close to Mr Obama - a direct meeting would have marked the first time in 43 years a US president had met a Burmese leader.
But the fact that a US president has sat down at the same table with a member of the Burmese military government is a clear sign that America is serious about wanting to re-engage with the region, says the BBC's Rachel Harvey in Singapore.
US presidents have previously refused to hold meetings with Asean when Burmese leaders were present.
The US has previously boycotted Asean meetings because of Burma.
"The president was just - as you know - in the scheduled meeting with the 10 Asean nations, and brought up in the meeting the... release of Aung San Suu Kyi by Burma. So, he brought that up directly with that government," Mr Obama's spokesman, Robert Gibbs said.
A joint statement released after the US-Asean talks, welcomed Mr Obama's policy of engagement with Burma and "underscored the importance of national reconciliation" there, but did not mention Aung San Suu Kyi.
"The general elections to be held in Myanmar in 2010 must be conducted in a free, fair, inclusive and transparent manner in order to be credible to the international community," the statement said.
Aung San Suu Kyi's party won Burma's last elections in 1990 but the military never allowed her to take power.
Observers believe Burma's authorities want to keep the pro-democracy leader in detention until after polls scheduled for next year.
The Obama administration has said it favours cautious diplomatic engagement, with sanctions against the regime remaining in place until real progress on democratic change is made.
Suu Kyi 'to be freed in November'
By Conor Duffy from Bangkok/ABC news online
Posted Mon Jan 25, 2010 7:24pm AEDT
Updated Mon Jan 25, 2010 10:39pm AEDT
Aung San Suu Kyi has spent much of the past two decades under house arrest. (AFP)
There are unconfirmed reports Burma's detained opposition leader Aung San Suu Kyi will be released from house arrest in November.
Aung San Suu Kyi has spent much of the past two decades under house arrest after winning Burma's last elections in 1990.
She has come to be seen as a symbol of democracy in a country that has endured two decades of oppressive military rule.
Today there are reports the Burmese home minister has told a gathering of local officials that Ms Suu Kyi will be released in November.
That is one month after the country's first elections in 20 years, which are expected to be held in October.
Burma's military government has so far not confirmed Ms Suu Kyi's release.
Burma frees defiant Suu Kyi deputy
Posted 2 hours 16 minutes ago/ ABC online news
Burma's junta has freed the deputy leader of Aung San Suu Kyi's opposition party from house arrest, prompting him to vow to resume his political activities ahead of elections later this year.
Tin Oo, 83, the vice chairman of the National League for Democracy (NLD), had been held without trial since 2003 when he and Suu Kyi were arrested after a pro-regime mob attacked their motorcade during a political tour.
His release on the day his current period of government-ordered detention expired came shortly before a UN rights envoy was due to visit Burma for talks focused on the polls promised by the ruling generals.
"The authorities informed me that they have withdrawn their restriction order," Tin Oo, appearing healthy despite his time in captivity, told reporters at his Rangoon home after police officers visited him to tell him the news.
Tin Oo said he believed that Suu Kyi, who has been in detention for most of the last 20 years and had her house arrest extended in August after an incident in which a US man swam to her lakeside house, would be freed "soon". ...<cont>
Suu Kyi's party boycotting Burma election
Updated 52 minutes ago?ABC news
Aung San Suu Kyi has been under house arrest for almost 14 out of the past 20 years. (Reuters: Sukree Sukplang, file photo)
Burma's opposition party led by Aung San Suu Kyi said it would boycott polls expected later this year, after the country's military rulers introduced a controversial new election law.
The National League For Democracy (NLD) decided at a party meeting to refuse to register for the first polls to be held in two decades, a move that would have forced it to oust its detained leader and recognise the junta's constitution.
But the NLD now faces dissolution in less than six weeks for failing to register, according to the new legislation brought in earlier this month for the elections, which are due to be held by the end of November.
"The National League for Democracy has decided not to register the party," party spokesman Nyan Win said after a meeting of more than 100 senior members at NLD headquarters in the economic hub Rangoon.
Under the internationally-criticised election legislation, if the party had decided to sign up for the vote it would have been forced to part with Ms Suu Kyi because she is serving a prison term.
The vote is part of the government's seven-step "Roadmap to Democracy", which also includes a controversial new constitution agreed in a 2008 referendum held days after a cyclone ravaged the country.
Burma's election legislation nullifies the result of the last polls held in 1990 that were won by the NLD by a landslide but never recognised by the junta.
If the party had registered it would have been forced to recognise that decision. ...<cont>
New Burmese opposition party to contest election
Former opposition leader Aung San Suu Kyi is not expected to join Burma's newly-formed National Democratic Force. Photograph: Hla Hla Htay/AFP/Getty Images
A faction of Burma's pro-democracy opposition movement said today that it will form a new political party to contest this year's elections.
The announcement came a day after the forced dissolution of the National League for Democracy, which won Burma's last election in 1990 but was prevented from taking power by the army.
The League declined to register for this year's vote, claiming that new election laws were unfair and undemocratic. Its non-registration was tantamount to an election boycott.
However, a group of League members who disagreed with the boycott said they would form their own party, the National Democratic Force.
"We will form a new political party to continue our struggle for democracy and human rights," said Khin Maung Swe, a former senior member of the League and a former political prisoner.
Whether the League's erstwhile leader Aung San Suu Kyi would play any role in the new party was not immediately clear, but it appears unlikely. She has called the junta's election laws undemocratic and said she would not think of registering her party for the polls.
Khin Maung Swe said he had suggested the idea of forming a "lifeboat party" to enable the League to circumvent the dissolution. "The idea was not accepted," he said.
He said the new party would register with the election commission this month. The law that imposed a registration deadline of 6 May applied only to existing political parties.
Than Nyein, who is expected to serve as the new party's chairman, said: "We are going to continue our unending democratic struggle within the legal framework."
On Thursday, officials at the National League for Democracy tidied their desks and locked files at their main office in Rangoon, a quiet end to a political party founded more than 20 years ago to challenge military rule. ..<cont>
Release Nobel winner, Obama tells Burma
June 20, 2010/Sydney Morning Herald.
Birthday wishes ... British ambassador to Indonesia Martin Hatfull speaks out for the release of Aung San Suu Kyi outside the embassy in Jakarta.
WASHINGTON: US President Barack Obama has called on the Burma regime to free Nobel Peace laureate Aung San Suu Kyi in a message sending best wishes for her 65th birthday.
Mr Obama hailed the Burmese opposition leader's ''determination, courage, and personal sacrifice in working for human rights and democratic change''. She spent her birthday yesterday under house arrest in Rangoon while global calls were made for her freedom at rallies and vigils.
The junta has kept Ms Suu Kyi in detention for almost 15 years and she has been barred from standing in coming elections that critics have denounced as a sham aimed at entrenching the generals' power.
''I wish to convey my best wishes to Aung San Suu Kyi, the world's only imprisoned Nobel Peace laureate, on the occasion of her 65th birthday on June 19,'' Mr Obama said.
''I once again call on the Burmese government to release Aung San Suu Kyi and all political prisoners immediately and unconditionally and to allow them to build a more stable, prosperous Burma that respects the rights of all its citizens.''
US State Department spokesman Philip Crowley echoed the President's wishes. He said freeing her and her fellow political prisoners would ''demonstrate a commitment to the brighter future the Burmese people so richly deserve and would help set the stage for true national reconciliation''.
The United Nations Secretary-General, Ban Ki-moon, has also demanded that Burma's military rulers release Aung San Suu Kyi.
She plans to celebrate her birthday by providing lunch for the three dozen construction workers helping to renovate her crumbling two-storey mansion, her lawyer, Nyan Win, said.
She cannot attend a birthday party planned in her honour at the suburban Rangoon home of a fellow opposition party official.
Ms Suu Kyi has spent 15 birthdays in detention in the past 20 years, mostly under house arrest. ''It is very sad that she cannot celebrate her birthday in freedom,'' said Nyan Win.
The National League for Democracy opposition party is planting 20,000 trees in Burma, mostly in Buddhist monasteries, to mark the occasion and will offer meals to monks as part of prayers for her release.
Suu Kyi's lawyer sceptical about release
Updated 5 hours 11 minutes ago
Scepticism over release claim: A Burmese pro-democracy activist during a protest in New Delhi (Reuters: Danish Ismail)
Lawyers for Burma's democracy leader Aung San Suu Kyi are sceptical about the junta's statement that it plans to release her next month.
A Burmese official told journalists Ms Suu Kyi will be released when her sentence is complete on November 13 - six days after the country's first election since 1990.
But Ms Suu Kyi's US-based lawyer, Jared Genser, has told ABC News Breakfast he has his doubts.
"The regime has publicly and repeatedly said that she was going to be released on prior occasions and then have not followed through on those promises," he said.
"So I tend to believe what I see the regime do, not what they say they're going to do."
He says Ms Suu Kyi has not been told she is going to be released.
"Neither she nor her lawyers have been told [by authorities] she's going to be released," he said.
"This is just information being provided by apparently mid-level government officials to a number of media enquires.
"I would imagine she, more than anybody, will be sceptical of the regime's intentions, given her personal experience over the last 20 years.
"I don't think anyone will be surprised either way."
Ms Suu Kyi has been in custody for most of the past 20 years since her party won a landslide at the last election in 1990.
Her party, the National League for Democracy, has now been effectively banned because Ms Suu Kyi was under house arrest and banned from political participation.
Video: ABC's Zoe Daniel reports from Burma
Source: ABC News
Published: Wednesday, November 3, 2010 8:24 AEDT
Expires: Tuesday, February 1, 2011 8:24 AEDT
The ABC's Zoe Daniel reports from Burma ahead of the nation's first election in 20 years.
Burma's junta claims election
Daniel Ten Kate and Supunnabul Suwannakij, Bangkok
November 10, 2010/the AGE
BURMA's military has claimed victory in the country's widely criticised first election in 20 years, saying it has won about 80 per cent of the seats.
''We have won about 80 per cent of the seats. We are glad,'' said a member of the Union Solidarity and Development Party, the junta's political arm, who did not want to be named.
The USDP member said turnout was more than 70 per cent, despite muted activity at polling stations on election day.
Thai authorities are in talks with Burma to return 15,000 people from ethnic minorities who fled fighting along the border that broke out after the polls, according to Samard Loyfar, governor of Thailand's adjoining Tak province.
The Democratic Karen Buddhist Army, one of more than 30 ethnically based militias based inside Burma, retreated after storming the Myawaddy-Mae Sot border crossing following the country's first vote in 20 years, he said. The thousands who fled Burma on Monday took refuge in temporary camps set up by Thailand's military.
''We are co-ordinating with Myawaddy provincial officials to send the people back to [Burma],'' Mr Samard said.
Thai intelligence officers confirmed that the rebel group left the area and no more gunfire had been heard since early morning, Mr Samard said.
The temporary camps in Thailand filled up on Monday night as more than two-thirds of Myawaddy residents fled, said Khin Ohmar, co-ordinator of the Burma Partnership, an umbrella organisation of civil society groups.
Local residents, migrant workers and Burmese pro-democracy activists who live in the area brought them food and blankets, she said.
''Everyone was sitting on the ground and I'm not sure they had space to lie down and sleep,'' said Khin Ohmar, who lives on the Thai side of the border in Mae Sot and visited the camps on Monday night. ''There were no facilities, no toilets, nothing.''
Thailand tightened border security and expects more attacks until the new government is set up, which could take three months, Prime Minister Abhisit Vejjajiva said yesterday.
The DKBA brigade is among ethnic militias resisting government efforts to turn them into border guards, as mandated by the 2008 constitution under which the elections were held. About a third of Burma's 55 million people belong to ethnic minorities.
''The ethnic armies are not happy with the election process,'' said Aung Zaw, who helped lead a 1988 student revolt and runs online magazine The Irrawaddy from his exile base in Chiang Mai, Thailand. Both the government and the militias ''are preparing for war instead of peace'', he said.
Several dozen ethnically based political parties joined Sunday's election, which was widely condemned as neither free nor fair.
Early returns showed that the National Democratic Force, the main pro-democracy party, may win almost half the 37 seats in Rangoon, the country's former capital.
The military will retain a quarter of the seats in the two houses of parliament, according to the constitution. Elected lawmakers in both houses can nominate a presidential candidate to compete against the military-appointed legislators' contender.
Uneasy Burma awaits Suu Kyi
Jack Davies, Rangoon
November 9, 2010/the AGE
WITH voting in the first general election in two decades complete, and the arcane process of counting votes and declaring a winner likely to take days, the people of Burma have turned their attention to another seminal democratic event - the expected release within days of their country's most famous democracy champion, Aung San Suu Kyi.
Legal opinion suggests Ms Suu Kyi, who has spent 15 of the past 20 years in prison or under house arrest, is due to be released on November 13.
''November will be an important and busy month for us because of the election and because of Aung San Suu Kyi's release,'' an unnamed official said in October.
There has been no suggestion on whether she will be allowed to join a political party, meet with supporters, or speak with the media. ...<cont>
Suu Kyi to be freed within days: officials
Updated 1 hour 11 minutes ago
Lawyers for Aung San Suu Kyi say her current term of house arrest is due to end on Saturday. (Reuters: Sukree Sukplang, file photo)
Unnamed officials say Burma's government is "certain" to release democracy icon Aung San Suu Kyi in the next few days.
"It's certain," said one official, speaking on condition of anonymity.
The Nobel laureate, who has been in detention for 15 of the past 20 years, is due to be released tomorrow when her most recent sentence is up.
The democracy campaigner has said through lawyers, however, that she will not accept conditions on her freedom.
If she is released it will come just a week after the first election since she and her party won in a landslide in 1990 but were never allowed to take power.
Meanwhile, it is understood that one of her sons has been granted a visa and is on his way to Rangoon.
Aung San Suu Kyi may be about to go free, but for how long?
After 15 years, the Burmese opposition leader is expected to be released from house arrest in less than 48 hours
.... Aung San Suu Kyi's first act as a free woman would be to address the Burmese people and speak to the media, local and international.
"She will make a press conference, she needs to speak to the Burmese people but the world too. This is what she always does."
She also wants to reinvigorate the National League for Democracy, the party she led to victory at the 1990 election but which has since been proscribed by the junta after advocating a boycott of last Sunday's poll.
All of this is certain to raise the ire of the junta's ruling generals. On past form, theirs and hers, Aung San Suu Kyi's liberty could be short-lived. "She never thinks of that. She will do what she needs to do. For her people like before, like always."
Aung San Suu Kyi 'will not be released until tomorrow'
Co-founder of National League for Democracy says impasse in negotiations with Burmese junta means pro-democracy leader will spend extra night under house arrest
guardian.co.uk, Friday 12 November 2010 12.47 GMT
Aung San Suu Kyi Aung San Suu Kyi will not be released until tomorrow, the National League for Democracy co-founder has said. Photograph: Khin Maung Win/AP
Aung San Suu Kyi appeared set to spend an extra night under house arrest as she negotiates the terms of her release with the Burmese junta, despite reports that she would be freed today.
The military regime – which has kept the pro-democracy leader and Nobel laureate locked up for the past seven years, and for 15 of the last 21 – signed an order this afternoon authorising her release from her latest period of detention.
Aung San Suu Kyi is understood to be demanding an unconditional release, but the regime is attempting to restrict her ability to travel around the country and limit her freedom to meet supporters.
At dusk in Rangoon, U Win Tin, the co-founder of her now-banned National League for Democracy (NLD) party, appeared at the military roadblock outside the gates of her house, where hundreds of supporters had gathered.
He said Aung San Suu Kyi had been told she "could go this day", but that it was likely it would be one more night before she emerged in public because of an impasse in negotiations. ...<cont>