After the Uprising of 1863, the commission was closed and replaced by the government-sponsored Vilnius Archaeographic Commission (copying the example of the Imperial Archaeographic Commission). It was chaired by Yakub Holovatsky in 1868–1888, in 1888–1902, and in 1902–1913. It was no longer in charge of the museum, which was subordinated to the . Instead, the commission focused on publishing historical material that would demonstrate that Lithuania was an ancient Russian and Eastern Orthodox land that needed to return to its roots (i.e. the official position to justify various Russification policies). The commission published 14 books and 39 volumes of "Acts of the Vilna Archeographic Commission" (Акты Виленской археографической комиссии), which published primary sources on the social and economic history. The documents included files from courts in Vilnius, Hrodna, Ukmergė, Upytė, Trakai, Minsk, Slonim (vols. 2–9, 22, 26, 32, 36), magistrates in Vilnius and Mogilev (vols. 10, 20, 39), Lithuanian Tribunal (vols. 11–13, 15), inventories of Lithuanian manors (vols. 25, 35, 38), documents on Lithuanian nobility (vol. 24), Lipka Tatars and Lithuanian Jews (vols. 28, 29, 31), Eastern Orthodox Church (vol. 33), Union of Brest (vol. 16), Russo-Polish War (1654–1667) and French invasion of Russia in 1812 (vols. 34, 37). Russian administration also established an archaeological commission, a local chapter of the Imperial Russian Geographical Society, but it was largely inactive.