A foetus, a two-year-old boy and a seven-year-old girl were among 117 human remains recovered from a mass grave made by Mexican authorities in 2014, according to the officials.
It took 12 days for forensic experts to dig the pit in the central state of Morelos. One more body than they previously believed was buried in a cemetery in Tetelcingo.
Morelos attorney general Javier Perez said authorities are investigating why they had a registry of 116 bodies instead of 117.
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The case has caused outrage in Mexico, where more than 28,000 people have disappeared in a decade of drug violence.
Perez said the foetus, a 36-week-old female — nearly full term — was found dead on a street in 2012 in the city of Cuernavaca. The seven-year-old girl was found on December 26, 2012, between Cuernavaca and Jiutepec, and an autopsy concluded that she had died of a contusion in the chest. The two-year-old boy was discovered in a river in April 2013, with his death caused by head trauma.
The bodies of the children were never claimed, Perez said.
The law allows authorities to bury bodies that remain unidentified and that nobody claims, but irregularities were found in the Tetelcingo case.
Some bodies were buried without a document with a case number, or the number was ineligible. Perez said 28 remains did not have a genetic registry.
The scandal erupted after a mother launched a legal battle to recover the body of her son, Oliver Wenceslao Navarrete Hernandez. Navarrete was found dead after he was kidnapped in 2013. His family was unable to bury him because prosecutors insisted on keeping the body for forensic tests.
But the body vanished from official records until an official revealed that Navarrete was buried in the mass grave with apparently falsified documents.
His family was present when officials opened the grave for the first time in December 2014, and they made a video of the grim dig.
But it was not until November 2015 that the discovery became public. Under pressure, authorities agreed to exhume all the bodies and open an investigation.
Two former officials from the state prosecutor’s office are under investigation.