Mexico's head of criminal investigation, who has faced a probe into his handling of the case of the disappearance of 43 students in 2014, stepped down on Wednesday.

Attorney General Arely Gomez accepted the resignation of Tomas Zeron as director of the Criminal Investigations Agency, the federal prosecutor's office said in a statement, two weeks before the tragedy's second anniversary.

Gomez "recognized the efforts" of Zeron as head of the agency and "wished him success in his personal and professional projects," the statement said.

The statement did not say why he had stepped down.

But parents of the missing students had called for his resignation over his conduct in the investigation of the disappearance of the 43 trainee teachers in the southern city of Iguala on September 26, 2014.

In April this year, the attorney general's office opened an internal investigation into Zeron's handling of a crime scene.

A federal government official told AFP that the inspector general's investigation is "ongoing."

The internal probe was launched after the foreign experts from the Inter-American Commission on Human Rights questioned the way a charred bone fragment linked to one of the 43 students was found in a river in October 2014.

The experts slammed Zeron's conduct, saying his failure to make a written report about the visit went against the "minimum international standards of investigation."

The commission's team also said medical reports show that a suspect who led Zeron to the river had injuries that strongly indicated he was tortured.

Zeron has vehemently denied any misconduct.

The bone belonged to the only student whose remains have been positively identified.

Authorities say the students were abducted by corrupt police officers who handed them over to the Guerreros Unidos drug cartel, which allegedly killed them.

Experts have repeatedly voiced doubts about the government's assertion that the cartel burned the bodies at a garbage dump before throwing the remains in a river, saying such a huge funeral pyre was implausible.

In September 2015, Zeron insisted that at least a "large group of students" were burned at the dump but that he could not "confirm that it was all 43."