They separated out Jewish POWs and sent them to the labor and death camps. We have survivor testimony. Some people died. Soviet Jewish POWs were treated particuarly badly (they were a large chunk of the original test for Zyklon B).
BTW, at least in the US, there was a lot of suspicions/basically they knew by the time D-day arrived. There were a LOT of discussions about what to do about the dog tags because they were marked H for jewish for burial reasons. For obvious reasons, if you read up on Jewish GI/watch documentaries/read memoirs/other material - they all talk about thinking about it and/or talking about the issue with friends and family if they went to Europe.
 the Reform movement, which at the time was the most powerful denomination in the US at the time, for some reason didn’t like the term Jewish and preferred Hebrew at the time (they were having A Moment). SO they basically had the most votes of the rabbinical council that advised the military (but at least they didn’t take over the siddur, that would have been…gah) This apparently caused a lot of head-scratching by the vast majority of American Jewish GIs, who were not reform (and even many who were Reform thought it was a bit weird. Today they say J, because there was a collective decision that the Hebrew thing was stupid.
They were treated like normal POWs. Badly, but not because they Jewish, but because they were POWs and Japan had feelings about surrendering and honor.
I suspect the reason is that outside of adopting some of europe’s distate for bolshevim, they had zero opinions of Jewish people, because both average japanese person and most of the government officials didn’t know any. They were random westerners and middle easterners for the most part, and very few made their way to Japan in the first place even in the modern period. Super tiny communities died out from attrition into the larger population. Even today, the population of Jewish people in Japan is extremely tiny (it ranges between 300-2k people total in the entire country - and is almost completely made up of ex-pats and foreigners)
Though this ended up working out in some surprising ways - the entire Mir Yeshiva ends up in Shanghai (though it ends up moving again out of China to Jerusalem after the war)
I just saw a documentary cover that. In Germany even allied pows who were Jews or even troublemakers to the concentration camps where they were worked to death. Dachau was one example based on testimony from soldiers and survivors. It however is a subject that has only come to the real light in the past few years.