Jews died in Holocaust...in Asia!

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The family still tells the story with pain. In the spring of 1947, shortly after his repatriation, Chitin. Sugihara was summoned to the Japanese Foreign Ministry in Tokyo. He was ordered at that time to tender his resignation, which he submitted on May 28. It was accepted on June 7, 1947.

"Since I would like to resign, please give permission to that effect. Signed, Sugihara." How voluntary this resignation was and what prompted it is not clear. The Foreign Ministry claims this he was given a termination fee of 7,605 yen and a starting pension of 1,617 yen.
The ministry further claims that this was a result of retrenchment. Indeed, whatever statistics we have on the Japanese government indicate large-scale forced resignations and particularly strong retrenchment in the diplomatic wing of the Foreign Ministry. An occupied country does not need many diplomats.

The family claim that Sugihara was forced to resign. He was being punished for the "Lithuanian incident." The claims are difficult to assess. What is clear is that Suffilura himself believed he was being punished.
In later years, he even told foreigners that he was listed as a criminal of war by the American forces. There is no evidence for this, notwithstanding his close relations with Hiroshi Oshima and Togo, who were subsequently placed on trial.

It also seems clear that an official forced to resign because of insubordination or any other criminal charges would not have been awarded a termination fee and lifelong pension. if his were truly deemed to be criminal behavior, he would have been punished long before.

But given Sugihara's second-tier status within the Foreign Ministry—not a graduate of Tokyo University—it is likely that he would be a prime candidate for forced resignation. Even with the democratization introduced by General MacArthur's staff, the Gaimusho was not a bureaucracy immediately reorganized to recognize achievement.

At the same time, there is no evidence that his visa-granting activities and some of the complications that they subsequently caused were an altogether neutral factor in forcing him to quit.
For years, his existence and his act were denied by Gaimusho officials; several people who tried to locate Sugibara attest to this. It could be that the Japanese officials who made the decision to fire Sugihara harbored some resentment, even based on Sugihara's rescue of Jews.
In search of Sugihara: the elusive Japanese diplomat who risked his life to rescue 10,000 Jews from the Holocaust by Hillel Levine

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Interestingly, Hillel Levine says that Sugihara risked his life, although, obviously, as a diplomat, he didn't.

"his close relations with Hiroshi Oshima and Togo" is interesting too.
It could have generated a feeling of inviolability.
After all, who would dare question the actions of a close associate of Shigenori Tōgō and Hiroshi Ōshima?

[WWII Germany were atheists]

As I understand it, the Jews who approached Sugihara in Kaunas were members of a Hassidic sect, followers of a certain rabbi who had been based in the eastern part of Poland and had moved to Lithuania when their home area had been occupied by the Soviets in September 1939. It remains unknown why he agreed to issue visas to them as well as to the Polish agents who were his main concern, but it is implausible that he foresaw that they would become victims of a future German invasion

I think it unlikely that those Jews would have been in any danger from the Soviet occupiers of Lithuania. The Soviets targeted Jews who were politically active as members of organisations regarded as hostile to the Soviet Union, and deported many of them after the full takeover and annexation of Lithuania in July 1940, but otherwise they did not harm the Jewish population as such. Jews in business and the professions had their property confiscated and lost their independence, but were usually rehired as managers of their former businesses or as employed professionals, provided they were not overtly anti-Soviet.

Religious Jews, particularly the ultra-Orthodox such as members of the Hassidic sects, were regarded by the Soviet occupiers as backward and superstitious, but not as dangerous, so they were not particularly persecuted, they just had their schools and institutions closed down.

After the war, Sugihara was dismissed from the Japanese consular service, and he subsequently claimed that it was because he had defied the wartime Japanese Government's regulations in issuing visas to Jews. However, the real reason for his dismissal was his involvement in anti-Soviet activities before the war, which made him persona non-grata to the first wave of US occupation officials, who were drawn mainly from the Department of State and were mainly very pro-Soviet and targeted Japanese officials who had been involved in anti-Communist and anti-Soviet activities. It was only in 1947, after the start of the Cold War, that the "reverse purge" occurred, with the pro-Soviet US personnel being replaced by anti-Soviet ones, who reinstated many of the purged Japanese officials. For some reason Sugihara was not one of those reinstated, and it seems unclear why.

1. there were some Hassidic sects that approached Sugihara but the majority were from anti-chasidic Orthodox Jews
2. I know jews who's ancestors were asked if they will give up Jewish practice and were deported in June 41 for refusing.
3. here is an audio from one of those ultra Orthodox who did not get get a visa and was sent with numerous others to Siberia
38:50 where he describes how his and others yeshiva were deported to Siberia,
https://collections.ushmm.org/search/catalog/irn507646