In Moscow, he earned the trust of Zigmas Angarietis and Vincas Mickevičius-Kapsukas, and became a member of the Central Committee of the Communist Party of Lithuania.

After the 1940 Soviet ultimatum to Lithuania and subsequent military occupation, Sniečkus was released from prison on 18 June 1940, and became the head of the Department of National Security.

Sniečkus helped create an atmosphere of terror prior to the elections of the newly established, by the Soviet authorities, People's Seimas, on 14 July.

It is estimated that in Lithuania five to ten thousand people engaged in Soviet underground activities during the war.

[3] In 1944, due to the advance of the Red Army, his mother fled Lithuania to the West, and disowned her son.

Sniečkus returned from Russia in 1944 with the Communist officials who had retreated during the German invasion of 22 June 1941.

At around this time his policies started to gain a nationalist character in the form of sabotaging some orders of Moscow and demanding some privileges for Lithuania and others.

[5] Sniečkus, a village for employees of the Ignalina Nuclear Power Plant on the shores of Lake Drūkšiai, was founded in 1975.