Prosecutors announced that the 116 bodies in the mass grave -- located in the town of Tetelcingo, just south of Mexico City -- were buried on March 28, 2014.
Activists are questioning the validity of the official record because authorities have files on only 88 bodies in the pits.
The unfenced rural grave consists of two adjacent 10-meter (33-feet) deep holes covering an area about six meters in length and four in width.
Morelos has been one of the Mexican states most affected by drug violence plaguing the country, including kidnappings and murders.
The United Nations along with several human rights organisations estimate that at least 20,000 people have gone missing in Mexico.
The head prosecutor in Morelos, Javier Perez, was among those witnessing the exhumation, which could last up to five days.
Dozens of relatives of the disappeared also attended, including Maria Concepcion and Amalia Hernandez, mother and aunt of the kidnapped and murdered Oliver Wenceslao Navarrete Hernandez.
After months of "many complaints and many battles," an official revealed that the victim's body had been buried in Tetelcingo "with signatures of false authorization," Hernandez told AFP. On December 9, 2014, a judge ordered his body be exhumed.
The body was found under dozens of others, "violating international protocols that indicate that in mass graves bodies must be separated from each other to allow eventual claims," said Roberto Villanueva, director of a program for victims at UAEM.
