The effort began more than a decade ago, the Serbian news agency Tanjug reported. The six-day exhumation in the Zadar city cemetery ended Friday.
Zadar is a city of about 75,000 on the Dalmatian coast northwest of Split.
The bodies will be returned to their families for reburial, officials said.
All the dead were killed in Operation Storm, a Croatian offensive in August 1995 that effectively ended the war. About 2,000 Serbs were killed and thousands more expelled from Croatia in a move Serbia describes as ethnic cleansing.