Skipitis work and activities were interrupted by the Soviet occupation in June 1940. Fearing an arrest by the NKVD, he fled to Nazi Germany in fall 1940. He left his wife and two daughters in Lithuania and they were deported to Siberia during the June deportation. In Berlin, he joined Kazys Škirpa and became one of the co-founders of the Lithuanian Activist Front (LAF) in November 1940. He was appointed chairman of the LAF commission on Lithuanians abroad. In April 1941, when plans were drawn for the June Uprising, Skipitis was reserved the seat of the Minister of Foreign Affairs in the Provisional Government of Lithuania. However, when Germany invaded the Soviet Union in June 1941, the Gestapo did not allow Skipitis to leave Berlin and he never joined the uprising in Lithuania. In July 1941, Skipitis, Ernestas Galvanauskas, and Petras Kalvelis petitioned Škirpa to close LAF in Berlin. Škirpa responded by officially dismissing the three from LAF.