From 4 March 1991 he was the Deputy Minister of Defence. On 31 March the Croatian War of Independence began between Croatia and the rebel SAO Krajina, supported by the Yugoslav People's Army (JNA). There were allegations that Šušak was in a group that had fired Armbrust anti-tank missiles on civilian houses in mostly Serb populated Borovo Selo in April 1991, prior to the Battle of Borovo Selo. On 25 June 1991, Croatia and Slovenia declared independence from Yugoslavia.