The 43 students were last seen being pushed into police vans after a protest in Guerrero state on September 26.
“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.
Angel 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 Angel Aguirre.
The students all attended a local teacher training college with a history of left-wing activism.
Six students were killed in two separate shooting incidents during the protests in Iguala, which lies some 120 miles south of the capital, Mexico City.
However, 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.
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