Mexico's attorney general has ordered the arrest of Jose Luis Abarca, Mayor of the town of Iguala, where 43 students went missing after clashing with police on 26 September.
The prosecutor accused Mr Abarca of ordering police to confront the students to prevent them from disrupting a public speech by his wife.
Six people were killed in the clashes and 43 students disappeared.
Eyewitnesses described seeing them being bundled into police cars.
Attorney General Jesus Murillo Karam said that arrest warrants had been issued for Mr Abarca and his wife, Maria de los Angeles Pineda, as well as the town's police chief, Felipe Flores.
Mr Abarca requested leave from his post following the incident on 26 September and neither he nor his wife or Mr Flores have been seen since.
They are now considered fugitives.
On 26 September, a group of students from a teacher training college in Ayotzinapa had travelled to nearby Iguala to protest against what they said were discriminatory hiring practices, and to collect funds for their college.
The college has a history of left-wing activism and according to Mr Murillo Karam, Mayor Abarca had been angered by a previous protest they had held in his town.
On the same day, Ms Pineda was giving a report to local officials about a programme offering social services to families, which she heads.
Local media have long speculated that the ensuing police crackdown on the students may have been related to Ms Pineda's public appearance.
In a news conference on Wednesday, Mr Murillo Karam said police officers testified that they had been told to intercept the students "on the mayor's orders" to prevent them from disrupting his wife's event.
Police then opened fire on the buses the students were travelling in, killing three of them and three more people in nearby vehicles.
One busload of students tried to flee but was stopped by the police and taken to Iguala police station.
Mr Murillo Karam also backed up claims that Ms Pineda and her husband had ties to a local drug gang calling itself Guerreros Unidos (United Warriors).
He said that the alleged leader of the gang, Sidronio Casarrubias Salgado, had accused Ms Pineda of being "the main operator of criminal activities in Iguala".
Mr Casarrubias, who was arrested last week in Acapulco, said the mayor had bribed local police to let the gang act with impunity and had even allowed gang members to infiltrate the force.
Mr Murillo Karam said the gang leader had described how the police turned the students over to the gang and how, upon receiving a message from one of his men describing them as members of a rival gang, he had ordered their disappearance.
The prosecutor said gang members then loaded them onto a pick-up truck and took them to Pueblo Viejo, where a number of mass graves have been found.
Forensic tests suggested 28 bodies found there were not those of the students, but Mr Murillo Karam said they "may have been flawed".
Mr Murillo Karam said two more bodies had been discovered since and Argentine forensic experts flown in to help with the investigation were carrying out further tests on all the bodies.
A total of 52 people, including police officers, local officials and gang members have been arrested in the case.