In November 1939, Merkys became Prime Minister. Raštikis resigned in January 1940 and was replaced by Vitkauskas. When Soviet Union presented an ultimatum on 14 June, Vitkauskas argued against armed resistance. The ultimatum was accepted and Lithuania lost its independence. Vitkauskas collaborated with the new regime becoming Minister of Defense in the People's Government, an elected delegate of the People's Seimas, and a member of the delegation that presented Joseph Stalin with a Lithuanian petition to become one of the republics of the Soviet Union. The Lithuanian Army was reorganized into the 29th Rifle Corps of the Red Army commanded by Vitkauskas. In June 1941, just before the German invasion of Russia, Vitkauskas was sent to the Military Academy of the General Staff in Moscow where he studied and later taught until early 1946. He returned to Lithuania and taught at the University of Kaunas and Kaunas Polytechnic Institute until retirement in 1954.