In August 1941, after the German invasion of the Soviet Union and German occupation of Lithuania, he returned to Lithuania and reorganized the Lithuanian Security Police in Vilnius (about 130 men) on Gestapo lines according to instructions he received in Germany, complete with a special division (Komunistų-Žydų Skyrius) for dealing with "Jews and Communists". The Lithuanian Security Police had jurisdiction over Jews in hiding, non-Jews who helped Jews, and Jews suspected of Communist associations. Usually, escaped or suspected Jews were arrested by the regular police and handed over to the security police for investigation and interrogation. The security police would then hand over the Jews to the German police or Ypatingasis būrys, a Lithuanian collaborationist death squad which murdered estimated 70,000 Jews at nearby Ponary. Acting as a desk murderer, Lileikis signed documents handing at least 75 Jews to Ypatingasis būrys. Lileikis fully understood that the Jews would be murdered. The Security Police also dealt with the Soviet partisans and Polish underground. For example, a report from 16 February to 21 March 1942 details that the security police in Vilnius arrested 319 people and 137 of them were sent to Ponary: 73 Jews, 23 Communists, 14 members of the Polish resistance, 20 document counterfeiters, and 7 spies. The duties related to non-Jewish groups increased as the number of Jews in the Vilna Ghetto dwindled and the anti-Nazi resistance grew.