On 15 June 1941, just a week before the Nazi German invasion of Russia, Vitkauskas was sent to the Military Academy of the General Staff in Moscow to complete courses for higher officers. It was part of a larger initiative to send Lithuanian officers to various courses and replace them with Russians. Two explanations are given – as a preparation for the German invasion or a precaution against a possible mutiny due to the June deportation. According to Vitkaukas' wife, the orders to depart to Moscow were urgent and Vitkauskas was placed under armed guard at the railway station. After the completion of the courses in December 1941, he taught tactics of the great military formations. He was a member of the Supreme Soviet of the Soviet Union from 1941 to 1954.