The post granted him effective command of the army in the Yugoslav federation, which crumbled after Slovenia and Croatia seceded in 1991.
He is now believed to be living in the US.
Croatian Serbs, armed and backed by Belgrade, opposed independence and created their own state in a war that killed and displaced thousands of people.
The conflict ended when a Croatian army crushed the rebellion in 1995.
Kadijevic is charged with responsibility for shelling civilian targets in the eastern Slavonia region, which borders Serbia.
He is also charged over atrocities committed by the Yugoslav army and Serb paramilitaries in the town of Vukovar, which they captured after a three-month siege in November 1991.
The Vukovar county court, which first indicted Kadijevic in 2002, reopened the case after media reported he had moved to the United States and was working as an adviser to the US army.
A court in nearby Osijek also indicted him.
The UN war crimes tribunal in The Hague, which deals with Yugoslav atrocities, charged six Yugoslav army officers for war crimes in Croatia but never indicted Kadijevic.
Bosnian Muslims arrested
Also on Thursday, Bosnia's police arrested two Bosnian Muslim wartime officials suspected of war crimes against Croats during the country's 1992-95 war of independence, officials said.
The state prosecution said it had ordered the arrests of Nisvet Gasal and Musajb Kukavica, former members of the Bosnian Muslim-dominated army.
"The arrested men are suspected of war crimes committed in 1993-94 against Croats in the area of [the central town of] Bugojno," Boris Grubesic, the prosecution spokesman, said.
The two men are the first Muslims arrested in connection with crimes against Croats in wartime detention camps in Bugojno.
Local media reported that Gasal had run the Stadion detention camp for Croats in Bugojno, with Kukavica his deputy.
Bosnian Muslims and Croats fought together against Serbs early in the Bosnian 1992-95 war, but then started their own war in 1993, which ended a year later.