Eighteen skulls appeared to have been violently shattered, the Phnom Penh Post reported.
Workers at the Wat Kesararam pagoda in the town of Siem Reap said arm bones were found bound together with rope and leg bones locked together with iron cuffs.
Chief monk Sambath Ly Ye said the temple had been built on a former Khmer Rouge execution site.
Human bones had been discovered at the pagoda in the past several years, he said, many buried with handcuffs. The remains are kept in a small cottage behind the temple.
A construction worker said more bones were first discovered last week, and many skulls and bones, "some already rotten," were found this week after a few feet of topsoil was removed to build living quarters for the monks.
Work at the site has now stopped.
Van Than Peou Dara, the deputy director of the Documentation Center of Cambodia, said the center's research had found the land on which the pagoda is now built had been a security office, prison and killing site during the Pol Pot regime.
Siem Reap District Governor Tep Bun Chhay said the deaths also could have occurred in the Lon Nol era.
Some 24 killing sites were known to exist in the province, he said, where an estimated 44,258 people were believed to have died.