He began to organize the International Jewish Anti-Fascist Committee. During this time he established contacts with Stanisław Kot, the Polish ambassador in Moscow, and called for Polish Jews in the Soviet Union to join the Polish Anders Army. In October 1941, Alter, together with Henrik Erlich were placed by the Soviet authorities in a hotel in Kuibishev (Samar). During private conversations, which were taped and reported to Joseph Stalin, the two discussed the rumors about the murder of Polish officers, including many Polish Jews, at Katyn. On 4 December 1941, he was again arrested by the NKVD, together with Erlich and murdered, although the precise details about his death are unknown. According to some reports, he was sentenced to death on 23 December 1941, and immediately executed. Other sources state that his execution did not take place until February 1943. The death sentence was signed by Vyacheslav Molotov in a note to Lavrentiy Beria, stating that Stalin had personally approved the order.