In 1926-1927, he was a director of the Lithuanian official news agency, ELTA. He later voiced opposition to the ruling elite in Lithuania; in this way, he became a suitable candidate for the Lithuanian communists (manipulated by Soviet envoy Vladimir Dekanozov) to become puppet Prime Minister of Lithuania in 1940 (June 17, 1940 July 21, 1940), when Lithuania had been occupied by Soviet troops. His appointment as Prime Minister was made under the control and dictate of the Soviet embassy in Kaunas. Aided by specialists sent in from Moscow, Dekanozov worked through the Lithuanian Communist Party, while the cabinet of ministers, headed by Paleckis, served an administrative function. Dekanozov and Paleckis brought a number of non-Communists into the first "People’s government", but in historical retrospect it is clear that they constituted window dressing for the Soviet takeover. In order to save face, the Soviet Union attempted to cover its annexation of the Baltic States with a cloak of legality. Therefore Moscow ordered the puppet government of Paleckis to carry out elections for a People’s Parliament on July 14-15 with a single list of candidates. The People’s Parliament was assigned the mission of introducing a Soviet regime in Lithuania and requesting admission into the Soviet Union.
It is considered to have been unconstitutional, especially since former state President Antanas Smetona had never resigned from his office. Justas Paleckis's peers were mostly NKVD residents in Lithuania (M. Gedvilas, M. Mickis). Paleckis personally signed the documents of mass deportation. With his agreement, former Prime Minister of Lithuania Antanas Merkys and Minister of Foreign Affairs Juozas Urbšys were deported to Russian SFSR. The intelligentsia and Lithuania's elite were considered as enemies and were among the first sentences to deportation or death.
During 1940–1953, some 132,000 Lithuanians were deported to remote areas of the USSR: Siberia, the Arctic Circle zone and Central Asia. They were not allowed to leave remote villages. More than 70 percent of the deportees were women and children. There were 50,000 women and 39,000 children deported to remote areas of the USSR. Some 30,000 of the deportees died there mostly because of slave work and starvation. Some 50,000 of the deportees were not able to return to Lithuania. During the same period, another 200,000 people were thrown into prisons. Some 150,000 of them were sent to the Gulags, the USSR‘s concentration camps, situated mostly in Siberia.
Justas Paleckis held this office, which was named, according to the Soviet constitution, the Chairman of the Supreme Soviet of the Lithuanian SSR, until 1967.
Justas Paleckis' last name became synonymous with that of a traitor in Lithuania and has the same reputation and connotation as Quisling's in Norway.