The Croatian minister for war veterans' affairs, Jadranka Kosor, said on Friday that some of the victims had been killed in the wake of the Second World War.
About 20 corpses have been exhumed from the Volaski Vrh pit, and about 10 corpses have been found in the Soric Krcevina pit at the depths between 82 and 87 metres.
Forensic teams have so far unearthed 145 mass graves containing the bodies of victims of the Homeland Defence War, according to the minister.
Croatia is still looking for 1,122 persons who went missing during the recent war.