National Security Commissioner Renato Sales confirmed the detention of Gildardo Lopez Astudillo, 36, calling him the “intellectual author” of the students’ disappearance.

He was arrested in the city of Taxco and is suspected of involvement in drug distribution, extortion and organised crime.

In November, the then attorney general Jesus Murillo Karam said Lopez Astudillo had informed his drug gang boss, Sidronio Casarrubias Salgado, that rivals were causing trouble in the city of Iguala. Casarrubias allegedly instructed him to defend their turf.

The government’s investigation maintains local police in Iguala illegally detained the students from the Rural Normal School of Ayotzinapa on September 26 last year.

They turned them over to the Guerreros Unidos gang, where the authorities say they were killed and incinerated at a rubbish dump.

However, family members continue to doubt the official account of what happened.

A recent report presented by a group of independent experts has discredited many aspects of the official inquiry, such as discounting the possibility that the bodies were burned on a giant pyre at the dump.

Authorities say they have identified the remains of two of the missing students.

The identification of the second victim, Jhosivani Guerrero de la Cruz, was announced on Wednesday.

A team of Argentine investigators also working on the case said on Thursday night that “serious questions” remain about the origin of samples that were tested and it does not consider the identification a definitive result.

Prosecutors say corrupt municipal police in Iguala abducted the students after the young men seized buses for their political activities.

The officers then handed them over to the Guerreros Unidos drug cartel, which killed them after confusing them with rivals and incinerated their bodies in a garbage dump near Iguala.