Amor Masovic, head of the Commission for Missing Persons, said experts are looking for the graves of Muslims killed early in the 1992-5 war in Zvornik by the Yugoslav army.
Other sources, according to Masovic, say the bodies could be linked to the 1995 Serb massacre of up to 8000 Muslim men and boys in Srebrenica.
He said the bodies could have been reburied in Zvornik to hide traces of the crime.
Huge mass grave
"It could be both. By its size, this could be one of the biggest mass graves found so far, possibly containing hundreds of bodies," Masovic said.
Bulldozers removed the upper, half-a-metre thick layer of earth from the site, which is 45 metres wide and 4.5 metres long in a hilly area off a main road.
The experts, who included UN war crimes investigators, worked under sweltering heat on Monday and found part of a skull.
The biggest mass grave found so far is in Glumina, where the bodies of 274 Muslims from Zvornik were found in 1998.
Masovic's commission and UN investigators also found several other mass graves, each containing several hundred bodies.
"But here we will not know for sure until we dig deeper and reach the bodies," Masovic said, adding the work was expected to last for several weeks.
"By its size, this could be one of the biggest mass graves found so far, possibly containing hundreds of bodies"
The Commission for Missing Persons
Many dead still missing
Out of 28,000 people missing from the Bosnian war, around 16,500 have been exhumed so far and 11,500 have been identified.
Masovic' commission exhumed over 130 bodies of Zvornik Muslims earlier this month from several smaller mass graves outside the town.
About 1300 Muslims from Zvornik went missing in the war and the bodies of about 500 have been found.
Also in July, the commission found what it believed were three mass graves near Zvornik.
It said bodies of the Srebrenica victims were dumped there before being removed to the suspected mass grave opened up on Monday.
Remains of about 5000 Srebrenica Muslims have been found so far.
Bosnian Serb wartime leader Radovan Karadzic and his military chief Ratko Mladic, both fugitives, were indicted for genocide in Srebrenica by the UN war crimes court.