When Lithuania was occupied by the Soviet Union in June 1940, Aukštuolis along other dignitaries greeted Vladimir Dekanozov, deputy of Vyacheslav Molotov, at the Kaunas Airport. He remained in Lithuania though his wife fled to Argentina and he used his diplomatic contacts to help Martynas Yčas escape to Berlin. After the Soviet takeover, Aukštuolis lost his job at the ministry but with a recommendation from Justas Paleckis (they worked together at the Lithuanian legation in Riga) obtained a job teaching Russian language at the Secondary School No. 1 in Panevėžys. He was one of the 17,500 Lithuanians deported to Siberia during the June deportation in 1941. Together with several other prominent Lithuanians, including former president Aleksandras Stulginskis and minister Stasys Šilingas, Aukštuolis ended up in Kraslag in the Krasnoyarsk Krai. In 1942, he and 16 other Lithuanians were once again arrested and accused of anti-Soviet activities. The NKVD recommended a death sentence, but the final sentence of 25 years in prison was announced only in February 1952 – almost three years after Aukštuolis death from tuberculosis and malnutrition in Dubravlag.