After the Soviet occupation of Lithuania in June 1940, Žemaitis continued his active service in the 617th Artillery Regiment, where he was the head of the regiment's school. At the beginning of the war between the Soviet Union and Nazi Germany, Žemaitis was at the proving ground of Varėna. After receiving the order to retreat to the east, Žemaitis and a group of soldiers consciously fell behind and surrendered to the Germans. He did not want to serve the Nazis, and therefore he retired and settled down in Kaunas. He worked as a technician of peat extraction.