The pits will now be inspected for more bodies, he said.
Al Jazeera's Rachel Levin, reporting from Mexico City, said the government has speculated that the deaths could be linked to the country's powerful drug cartels.
But she said that is difficult to prove.
"In order to do successful DNA testing on these bodies the government would have to have a database of DNA of the families members of the bodies, and they don't have such an extensive database.
"What often happens in these situations is that these bodies are never identified. So we don't really know who they are or why they ended up there."
It is not clear how the dumping-ground was discovered. Drug related killings have become increasingly common in Mexico in recent years, with cartel hit men known to use mass dumping sites to dispose of their victims.
In May, police in the central Mexico tourist town for Taxco found 55 bodies in an abandoned silver mine.
The Mexican government has taken a hard line against the drug cartels, launching a major offensive against them in 2006.
But the operation has had limited success, with almost 25,000 people being killed since the operations began.
Felipe Calderon, the Mexican president, described the gangs as the "greatest threat to the well-being and progress of Mexican families".