Glavas left the prison hospital at 1815 hours in an ambulance that was taking him to a hospital in his home town of Osijek.
Lawyer Ante Madunic told reporters that his client was exhausted, but in a good mood, and that he was using a walking stick.
"Glavas should now be left to recover, after which the proceedings will resume," Madunic said, adding that his client's recovery would take a long time. "There's no reason for rejoicing. (...) We will prove that the accusations against Branimir Glavas are not true and we will prove the truth about the Homeland War."
Madunic said that Glavas proved with his hunger strike that he was a persistent person.
Glavas was sent off by a group of citizens and friends who had rallied outside the hospital to demonstrate their support.
The 11 war veterans, who went on a hunger strike outside the hospital about a week ago in support of Glavas's demand for provisional release pending completion of the investigation, stopped their strike today.
Glavas started a hunger strike on October 26 when he was remanded in custody on suspicion of involvement in war crimes against civilians in 1991. Today was the 37th day of his hunger strike.