Later he served as a Lithuanian representative to Germany (1927–1930), League of Nations (1937), Poland (1938), and again Germany (1938–1941). After Soviet Union occupied Lithuania in 1940, Škirpa fled to Germany and formed the Lithuanian Activist Front (LAF), a short-lived resistance organisation whose goal was to liberate Lithuania and re-establish its independence by working with the Nazis. According to Victims of Communism Memorial Foundation, he was a primary source of the secret part of the Molotov–Ribbentrop Pact which he sent to the Latvian foreign minister in 1939. When Nazis invaded the Soviet Union in June 1941, many members of LAF cooperated with the Nazis and killed thousands of Lithuanian Jews (see the Holocaust in Lithuania). He was named prime minister in the Provisional Government of Lithuania; however, the Germans placed him under house arrest and did not allow him to leave for Lithuania. He moved from Berlin to southern Germany and was allowed a short visit to Kaunas only in October 1943. In June 1944, he was arrested for sending a memorandum to the Nazi officials asking to replace German authorities in Lithuania with a Lithuanian government. He was first imprisoned in a concentration camp in Bad Godesberg and in February 1945 was moved to .