More remains are expected to be found near 65 of the graves which were uncovered in Putumayo province on the Ecuadorean border late on Friday.
A total of 211 bodies have been recovered from the province since last year, but Friday's find by agents from Colombia's attorney-general's office marked the most number of bodies found in a single area.
More than 31,000 paramilitaries have disarmed since 2003 under a deal promising reduced jail terms to those who co-operate with investigations into crimes they committed in the name of fighting Marxist rebels.
Both the "paras" and the rebels are funded by Colombia's multibillion-dollar cocaine trade and are branded terrorists by Washington.
The paramilitaries were organised in the 1980s by rich Colombians to fight the rebels.
By the late 1990s the conflict had turned into little more than a turf war over drug-smuggling routes.