Felipe Flores was detained at 7 AM in Iguala in an operation involving federal police, the military and the attorney general's office, the National Security Commission said on its Twitter account, without providing more details.
Flores was Iguala's police chief when officers attacked dozens of students in the town on September 26, 2014, after the young men stole buses for a protest in Mexico City -- a common practice among the trainee teachers in Guerrero state.
Prosecutors have said that the police officers took 43 students and handed them over to the Guerreros Unidos drug cartel, which killed them, incinerated their bodies at a garbage dump and tossed the remains in a river.
But the government's conclusions were rejected by independent experts from the Inter-American Commission on Human Rights, who said there was no scientific proof that the students were burned at the dump.
The attorney general's office has since agreed to look at other lines of investigation and conduct new searches.
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