Prosecutors also announced they had issued arrest warrants in the case against 20 army soldiers and officers, five local officials, 33 local police officers and 11 state police, as well as 14 gang members.
The roundup included the first arrest of a former attorney general in recent history, and one of the biggest mass arrests ever by civilian prosecutors of Mexican army soldiers.
Jesús Murillo Karam served as attorney general from 2012 to 2015, under then President Enrique Peña Nieto.
The office of the current attorney general, Alejandro Gertz Manero, said Murillo Karam was charged with torture, official misconduct and forced disappearance.
In 2020, Gertz Manero said Murillo Karam had been implicated in “orchestrating a massive media trick” and leading a “generalised cover-up” in the case.
The arrest came a day after a commission set up to determine what happened said the army bore at least partial responsibility in the case.
It said a soldier had infiltrated the student group involved and the army didn’t stop the abductions even though it knew what was happening.
Corrupt local police, other security forces and members of a drug gang abducted the students in the city of Iguala in Guerrero state, although the motive remains unclear eight years later.
Their bodies have never been found, though fragments of burned bone have been matched to three of the students.
Murillo Karam, under pressure to quickly solve the case, announced in 2014 that the students had been killed and their bodies burned at a garbage dump by members of a drug gang.
He called that hypothesis “the historic truth.”
But the investigation included instances of torture, improper arrest and mishandling of evidence that has since allowed most of the directly implicated gang members to walk free.
The incident occurred near a large army base, and independent investigations have found that members of the military were aware of what was occurring.
The students’ families have long demanded that soldiers be included in the investigation.
On Thursday, the truth commission looking into the case said one of the abducted students was a soldier who had infiltrated the radical teachers’ college, yet the army did not search for him even though it had real-time information that the abduction was occurring.
It said the inaction violated army protocols for cases of missing soldiers.
The defense ministry has not responded to a request for comment.
The soldiers and officers being sought under Friday’s warrants, and the other officials, police and gang members, face charges of murder, torture, official misconduct, criminal association and forced disappearance
It was not immediately clear whether all the suspects faced all the charges or if the suspects were among dozens previously arrested and charged during previous investigations.
Prior to reforms in Mexican law, the army had long been allowed to refer soldiers accused of wrongdoing to separate military courts.
But soldiers must now by tried in civilian courts, if their offenses involved civilians.
The soldiers being charged served at the base near where the abduction occurred in 2014.
The Institutional Revolutionary Party, which both Murillo Karam and Peña Nieto belonged to, wrote in its Twitter account that Murillo Karam’s arrest “is more a question of politics than justice. This action does not help the victims’ families get answers.”
Mexican federal prosecutors previously issued arrest warrants for members of the military and federal police as well as Tomás Zeron, who at the time of the abduction headed the federal investigation agency, Mexico’s detective agency.
Zeron is being sought on charges of torture and covering up forced disappearances. He fled to Israel, and Mexico has asked the Israeli government for help in his arrest.
Gertz Manero said that in addition to Zeron’s alleged crimes connected to the case, he is alleged to have stolen more than $US44 million ($AUD63m) from the Attorney General’s Office budget.
The motive for the students’ abduction remains a subject of debate.
On Sept 26, 2014, local police from Iguala, members of organized crime and authorities abducted 43 students from buses.
The students periodically commandeered buses for their transportation.
Murillo Karam claimed the students were turned over to a drug gang who killed them, incinerated their bodies at a dump in nearby Cocula and tossed the burned bone fragments into a river.
Later investigations by independent experts and the Attorney General’s Office, and corroborated by the truth commission, have dismissed the idea that the bodies were incinerated at the Cocula dump.
There has been no evidence that any of the students could still be alive.