There are reports that, through classified code-breaking efforts, US intelligence knew that there were Japanese spies among us, including who they were. But we couldn’t arrest them, only, without compromising the fact of the code-breaking. So, under the cover of clumsy and oppressive domestic policy, *all* citizens of Japanese descent were interred, thereby both neutralizing the threat as well as concealing the fact of our ability to decrypt Japan’s codes.
http://hnn.us/articles/9289.html
Japanese Internment: Why It Was a Good Idea—And the Lessons It Offers Today
That would make, though the books I have read did not discuss that as a reason. We had a similar problem with German spies, but the source was often the British. One way J. Edgar Hoover dealt with that was by giving British intelligence a much freer hand than he should have.