Specialists said on Monday that the bodies and body parts had been moved to a remote grave near the eastern Bosnian town of Zvornik to hide traces of mass killings.
"We have found dozens of bodily remains - some complete, some incomplete - and for now we are sure that this is a secondary grave," said Murat Hurtic, head of an expert team from the Commission for Missing Persons.
Hurtic said experts had found one skull with a bullet hole which meant the victim was shot from close range.
They also found the remains of women and children.
Biggest mass grave
"We think it will also be one of the biggest mass graves by the number of the remains found"
head of expert team, Commission for Missing Persons
"We believe it is one of the biggest, by area it certainly is, and we think it will also be one of the biggest mass graves by the number of the remains found," Hurtic added.
Experts believe Muslims from Zvornik and Srebrenica, captured by Bosnian Serb forces early in the war in a wave of ethnic cleansing, may have been dumped at the Crni Vrh mass grave.
Forensic specialists and court officials are working in the 40-metre by five-metre grave, deep in woodland, removing earth from dozens of piles of clothes, bones and shoes.
The week-old exhumation is expected to last at least another month.
The biggest primary mass grave uncovered so far was near Glumina, which contained 274 bodies.
More than 500 remains of Muslims from Srebrenica, where Bosnian Serb forces killed up to 8000 boys and men in 1995, were found in Kamenica, the biggest secondary mass grave.
About 1300 Muslims died in Zvornik and the bodies of some 500 have been found, including 130 exhumed last month.
Of 28,500 people missing from the Bosnian war, mostly Muslims, around 16,500 have been exhumed and 11,500 identified.