The group said in a statement that Sabaliauskas and CFO Simonas Klimavicius had been sacked after "losing the management board's confidence".
Irma Kamarauskiene, director of the group's Economics Department, took over as CFO.
Sabaliauskas would not comment on his dismissal on Wednesday.
Kanapeckas had held the post of the Control and Internal Audit Department at Achemos Grupe since 2014.
This is the eight top management change at Achemos Grupe since the death of Bronislovas Lubys, the group's founder and majority shareholder, in 2011.
The group controls more than 40 companies in Lithuania and abroad, including the fertilizer manufacturer Achema, the stevedoring company Klasco and the fertilizer trade and agribusiness company Agrochema, as well as a number of media organizations and hotels, and a wind farm in western Lithuania.
