In 1939 Chiune was then sent to the Japanese Consulate in Lithuania. On September 1st of that year Nazi Germany invaded Poland and the persecution of Jews began almost immediately.
By 1940 Jewish refugees from Poland and from within Lithuania itself began to seek ways to flee the country. This required visas and many countries were refusing to issue them. Japan itself had stringent requirements that the refugees did not meet. Chiune inquired to his superiors three times requesting instructions, but in all cases requests to issue the visas were declined.
It might have been easier to simply walk away and do nothing but instead, in July of 1940, against orders, Sugihara started issuing visas and even directly negotiated with officials of the Soviet Union to allow the refugees to pass through Russia on their way to Japan. He continued to write visas, reportedly spending 18-20 hours a day until September 4th when the Consulate was closed. During the night prior to the closing, Chiune and his wife Yukiko spent the entire night writing visas, and Chiune was reportedly even preparing them en route to the train station where he threw them out the window of the train to waiting refugees as it left the station. In a final act of desperation he resorted to throwing blank pages with the Consulate seal and his signature, which could be filled out later.
The exact number of Jews saved by Chiune Sugihara is not known but estimates put the number around 6,000.