General Djuro Brodarac died at the Clinical Hospital Centre in the eastern city of Osijek shortly after 8am on Wednesday, his lawyer Petar Sale confirmed to press.
Brodarac was hospitalised on Tuesday, but the exact cause of death was not immediately known. An investigating judge has ordered an autopsy.
Brodarac has been in investigative custody in Osijek for the past three weeks along with two other persons on the suspicion that they committed war crimes in the Sisak area in the early 1990s.
"Those who put him in prison were aware of his ill health because they had all the documents and they should have granted him provisional release or transferred him to hospital in time," Sale said.