After the Soviet occupation of Lithuania in June 1940, Šliūpas was invited (most likely via Mečislovas Gedvilas who was a member of the Society of Ethical Culture) to the People's Government of Lithuania, but refused. Former Prime Minister Antanas Merkys stopped by Šliūpas home in Palanga when he tried to flee abroad. Unlike many Lithuanian periodicals, "Laisvoji mintis" was not abolished by the new communist regime but Šliūpas was replaced as editor by . Šliūpas' investments and other property was nationalized, but the new government made a special exception allowing him keep his house in Palanga. During the June deportation, Šliūpas sister-in-law was deported to Siberia and he received a warning that his own family was on a deportee list.