One person two letters OR two persons one letter each?

They could have been more explicit. "A reference letter from two scientists in a related field" would be better for clarity, but the original is acceptable and should have been understood. Sometimes, you just have to think the requirement over and ask yourself why they would want two letters from one person. They could better have written "Two reference letters written by scientists in a related field".

Sorry I couldn't give much support. By the way, I don't know about Japan, but in the US, you wouldn't get the job by proving they had an unclear way of writing. Otherwise, I think you could win the argument on grounds of syntax.

It's simple logic really. If the reference letters are going to the same place, what is the benefit for the hiring company in having two of the letters coming from the same person. When the recommendation letters are from two different people within the same field, the company can gauge you better and get a varying perspective on you, since the content of the letters will be different when the letters are written by different authors.
Think about it, two recommendation letters from the same person to the same company will cover the same ground, thus you likely are not making the best use of your application.

I agree completely. Yagi could still make an arguement on the syntax, since scientist is singular, but as I mentioned, you don't get jobs that way.

@roger, @Enzo
Thanks for your comments. All right, in that sense, it’s partly my bad. But still, we are often asked “two copies of documents” or even five sometimes. Yes, it happens on the application but never on the recommendation letter. As Roger said, research organization is also singular. That made me thoughtless.

I accept your criticism. And now grammatical question was solved. Thanks guys.