In spring 1918, authorized by the Council of Lithuania, Sidzikauskas organized the evacuation of Lithuanian students and teachers back to Vilnius. The first Lithuanian government was formed only after the Armistice of Compiègne in November 1918. Leonas became Minister of Justice and invited Sidzikauskas to join the newly established ministry. Sidzikauskas agreed and was promoted to director of the Administration Department on February 1, 1919. In March, Sidzikauskas, as a representative of the Democratic National Freedom League, was a member of a six-men commission that negotiated the formation of the coalition Cabinet of Prime Minister Mykolas Sleževičius. Due to lack of personnel, he was also acting director of the Civil and Criminal Law and the Prisons Department. In this capacity he had to deal with communist prison riots and to arrange prisoner exchange with the Lithuanian Soviet Socialist Republic. On 24 July, he personally traveled to Daugailiai on the Lithuanian–Soviet front to exchange 15 prominent Lithuanians, including Mečislovas Reinys, Liudas Gira, Felicija Bortkevičienė, Antanas Tumėnas, for 35 communists.