The Morelos state prosecutor's office launched an investigation following the release of a video showing forensic officials in white protective suits exhuming bodies in the village of Tetelcingo.
The video was recorded in December 2014 by a murder victim's family, which had sought the exhumation of his body. The corpse was among some 150 others that had been buried in the pits in 2013.
"We will review whether (the forensic officials) acted within the protocols required by law," Morelos chief prosecutor Javier Perez told reporters.
The bodies had not been all identified and had been kept in morgues of the prosecutor's office, he said.
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While the forensic services can bury bodies in mass graves, there are a series of legal, health and administrative procedures to follow, Perez said.
"Unfortunately, the forensic services of the prosecutor's office do not have a big enough area" to hold many bodies, he said.
The state's human rights commission began its own investigation in Tetelcingo on Friday and said more than 140 bodies were dumped in the pits.
Rodriguez was kidnapped in May 2013 and his body was found 10 days later in a ravine.
The family recorded the exhumation despite the opposition of the authorities. The relatives said they counted 150 bodies wrapped in plastic and most lacked a file number.
Morelos has been one of the Mexican states most affected by drug violence plaguing the country, including kidnappings and murders.