“We feel the government’s priority is no longer finding the truth about what happened to the students, but is much more concerned with hiding the reasons behind a historical cover-up,” Mr. Patrón added.

The students’ disappearance has shaken the government of President Enrique Peña Nieto, becoming emblematic of Mexico’s inability to provide security to its citizens and its failure to confront the corruption that riddles law enforcement.

Outside experts have repeatedly raised questions about the government’s handling of the investigation in the weeks after the students vanished in September 2014, prompting the internal review.

The first version was completed in August but was never approved by the attorney general. It was obtained by The New York Times in December.

The students’ families were quick to condemn what they said was an attempt to whitewash the internal investigation.

“The problem is that the evidence was tampered with and the entire investigation has been manipulated and now they are denying the right to truth of 43 families,” said Mario González, the father of one of the missing students.

Mexican prosecutors have contended that the students were dragged off buses by local police officers and handed over to a drug gang, which killed them and burned their bodies at a garbage dump. Gang members were ordered to scoop the ashes into plastic bags and throw the bags into a river.

But the government account rests largely on confessions from people suspected of being drug hit men swept up in a dragnet around the southern city of Iguala, where the students, who attended a rural teachers’ college, disappeared.

Last year, a group of experts with the Inter-American Human Rights Commission cast doubt on much of the evidence underpinning the government’s version.

The five experts uncovered detailed evidence showing that 17 key suspects were tortured and that commanders at the local army battalion and the federal police were aware of the police attacks on the students but stood by. The experts’ group discarded the theory that such an intense fire could have taken place in the garbage dump.

Finally, they discovered that the lead investigator, Tomás Zerón de Lucio, had taken one of the suspects, Agustín García Reyes, to the bank of the San Juan River on Oct. 28, 2014, without recording the visit in the case file.

A bone found at the riverbank the following day was identified as belonging to one of the students, raising suspicions among the families that the evidence was planted.

Mr. Zerón’s unrecorded visit led to the internal review by the attorney general’s inspector general. Although the families were told they would see the review on Aug. 18, it was withheld at the last minute and never released. The inspector general, César Alejandro Chávez Flores, abruptly resigned four weeks later. The attorney general at the time, Arely Gómez, resigned in October to become the federal comptroller.

That first review painted a sweeping picture of dysfunction, the first time that the government itself had acknowledged the errors in its investigation.

Six key suspects were picked up over the course of a day and spontaneously confessed in identical wording to being members of the local drug gang Guerreros Unidos. Their subsequent arrests, based on those statements, were arbitrary and illegal, the first review found.

Mr. Zerón also took Mr. García Reyes to the riverbank without a defense lawyer, and then left the crime scene unguarded overnight, the review found. Dates were muddled, documents missing.

The review concluded that Mr. Zerón’s misconduct, along with the actions of prosecutors and forensic technicians in the days before and after the riverbank visit, violated the victims’ right to justice. It called for further investigation to determine if the misconduct warranted criminal penalties.

But the final report read very differently.

It maintained that the arrests of the six suspects were legal and contended that Mr. Zerón’s riverbank visit was only an administrative infraction.

The inspector general who replaced Mr. Chávez Flores, Adriana Campos López, told the victims’ parents that investigators were in a hurry to solve the case, spurring Mr. Zerón’s visit to the riverbank. Mr. Zerón has defended his actions as legitimate police work.

The final review, which refers his administrative sanction to the federal comptroller’s office, takes the same position.

But the families were unwilling to accept such reasoning.

“The new inspector general gave us a resolution that basically makes fun of the 43 students’ families,” said Mr. González, the father of one of the students.

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