In a statement carried by Dnevni Avaz daily of Sunday, Masovic said that there were also more than 1,500 individual graves which had to be investigated.
This year the Commission plans to exhume the remains of some 2,000 victims.
This year's priorities are the area of the northern town of Prijedor, where some 1,000 people are still listed as missing, and the Drina River area, Masovic said.
Some 16,000 people are still held missing in Bosnia-Herzegovina, but Masovic believes that this figure is not reliable considering that some 6,000 bodies exhumed so far are waiting for identification.
Since the signing of the Dayton peace agreement in 1995 the authorities of the Federation of Bosnia-Herzegovina have exhumed 13,915 victims from 363 mass, 200 common and more than 3,800 individual graves.
The remains of 748 victims were discovered in 20 pits, some of which were up to 80 metres deep.
Around 4,000 victims were exhumed by investigators of the Hague war crimes tribunal.
Bosnian Croat investigators performed independent exhumations for a certain period of time, during which they exhumed an additional 659 bodies, which brings the number of exhumed victims to 18,500.