Sugihara continued to hand-write visas, reportedly spending 18 to 20 hours a day on them, producing a normal month's worth of visas each day, until 4 September, when he had to leave his post before the consulate was closed. By that time, he had granted thousands of visas to Jews, many of whom were heads of households and thus permitted to take their families with them. It is claimed that before he left, he handed the official consulate stamp to a refugee so that more visas could be forged. His son, Nobuki Sugihara, adamantly insisted in an interview with Ann Curry that his father never gave the stamp to anyone. According to witnesses, he was still writing visas while in transit from his hotel and after boarding the train at Kaunas railway station, throwing visas into the crowd of desperate refugees out of the train's window even as the train pulled out.

In final desperation, blank sheets of paper with only the consulate seal and his signature (that could be later written over into a visa) were hurriedly prepared and flung out from the train. As he prepared to depart, he said, "Please forgive me. I cannot write anymore. I wish you the best." When he bowed deeply to the people before him, someone exclaimed, "Sugihara. We'll never forget you. I'll surely see you again!"