While I can't talk too much about the claim itself, it should be noted that the Japanese military was rather dysfunctional, and often times decisions would not be made the "normal way"-namely, by passing up information through the chain of command, and orders going down-but instead acted upon by the local commander on the scene. This can be seen for instance from 1931 where a colonel decided to unilaterally conduct foreign policy by invading Manchuria. This dysfunction certainly applied to treatment of prisoners as well. US Marines who were taken prisoner in China immediately after the commencement of hostilities were treated very well (some of them even being released in a few months, during the war!) compared to their comrades from Wake Island, who were treated quite poorly, such to the point that the two groups were alienated from each other when they were placed in the same camp.

In other words, it is entirely possible that if the Japanese imprisoned an American national, that the Japanese high command or the Japanese government would have absolutely no idea whatsoever. This if anything would be par for the course.

Follow-up question: When others have postulated that Amelia Earhart was shot down and/or captured by the Japanese, the reason was that she may have seen Japanese fortifications, fleet movements, or otherwise something the Japanese didn't want her to see. The implication to me always was that, had she gotten away, she could have tipped off the U.S. about Japan's intentions for war.

But this is four years before Dec. 7, 1941 -- do we now know of anything going on in that area of the Pacific that would have been a state secret worthy of capturing a world-famous aviator? Saipan had been awarded to Japan at the end of World War I, so a Japanese presence there wasn't a secret.