A total of 43 students went missing after clashing with police on September 26 in the town of Iguala
He was arrested in Iguala, in the southern state of Guerrero, where the incident happened.
Mexican government says the students were arrested by police before being handed over to a drugs cartel who killed them and incinerated their bodies.
Families and independent experts contest this claim.
The panel of experts, working for the Inter-American Commission on Human Rights, said the account that the students had been burnt beyond identification at a rubbish dump was physically impossible.
Felipe Flores was police chief of Iguala when the incident took place on September 26, 2014, and his arrest may offer new clues as to what exactly happened then.
Attorney General Arely Gomez welcomed Felipe Flores’ capture, tweeting that it would allow investigators to get “a fundamental statement to clear up the events”.
The case has tainted Mexican President Enrique Pena Nieto’s image.
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