Jews were not persecuted per se in Japan. While Japan was allied with Hitler, it preferred instead to utilize what it saw as the Jews' world economic and political power. They absorbed anti-Semitic material through their dealings with Russia, leading them to get misleading and outsized ideas of Jews' money and power, but put their own spin on it in which they decided to attempt to use Jewish influence to bring Jewish money into Japan-occupied China and improve relations between Japan and the US. Two Japanese officials, Yasue Norihiro and Inuzuka Korishige, spent years looking into "the Jewish problem" and ways that they could manipulate and utilize it. Japan ended up harboring many Jewish refugees in Japanese-controlled Shanghai, some who were already there, some who had been granted visas by Chiune Sugihara, a Japanese consul in Vilnius, Lithuania who gave visas to Jews in an attempt to save them, and some who had been granted visas by Chinese consuls in Europe (particularly Vienna) in order to save them; however, they did not do so due to a particularly good feeling toward Jews- but rather due to a belief that they could use the Jews for their own purposes. Yasue and Inuzuka respectively had authority in Manchuria and Shanghai, and allowed Jews to reside there for multiple reasons, including to provide good optics to the US, to get better access to Jewish money, and to get the sympathy and alliance of Jews in the US, Europe, and East Asia. These plans were largely made before the Tripartite Agreement with Germany and Italy- after this, and later on after Pearl Harbor, the Japanese lost a lot of their incentive to win over the US and put Jews in China and Japan into a ghetto in Shanghai. They never, however, murdered Jews as did Germany- or turned Jews over to be murdered as did Italy.

Further reading:

Gao, Bei, Shanghai Sanctuary: Chinese and Japanese Policy toward European Jewish Refugees during World War II