12 October 2014 Last updated at 01:38 
The 43 students were last seen being pushed into police vans after a protest in Guerrero state on 26 September.
“I can say that some of the bodies, according to the work of forensics experts, do not correspond to the youths,” said Governor Angel Aguirre.
Prosecutors believe police turned over the students to a drug gang.
The gang was linked to the family of Iguala’s Mayor Jose Luis Abarca Velazquez.
He, his wife and his head of security went on leave after the clashes and have not reappeared.
A formal search has been launched for them.
Mr Aguirre has promised new developments in the investigation over the next few days.
“I have big hopes of finding our young students alive. That is why we have now entered a new phase in the search for them,” he said.
The clandestine graves were located in the outskirts of Iguala following an anonymous tip off.
Twenty-eight burnt bodies were retrieved from the pits. Forensic experts are still working to identify all of them, said Mr Aguirre.
‘No impunity’The students all attended a local teacher training college with a history of left-wing activism.
Federal forces have disarmed local police and taken over security in the town of Iguala 
Parents of the students joined the search for their loved ones, but many fear the worst at this stage Six students were killed in two separate shooting incidents during the protests in Iguala, which lies some 200km (120 miles) south of the capital, Mexico City.
But it is not clear whether they were targeted for their political beliefs.
Some think that they may have angered a local drug gang called Guerreros Unidos by refusing to pay extortion money.
Thousands of people have taken to the streets across Mexico to demand government action to locate the students.
President Enrique Pena Nieto went on national television to promise to identify and punish those responsible for the disappearance.
He described the incident as “shocking, painful and unacceptable” and said there will be “no impunity”.
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Mexico bodies "not all students"
