It is not clear whether the bodies found in a pit are those of the missing students, who were last seen being forced into police vans.
The group had travelled to the area, in the state of Guerrero, to take part in a protest over teachers' rights.
Police opened fire on their buses, killing six people.
Twenty-two police officers are being held in connection with the shooting.
Witnesses said that most of the survivors - all trainee teachers - were bundled into police vans before disappearing.
Some had gone into hiding and contacted their relatives after several days, still fearing for their lives.
'Anonymous tip'It was thought initially that 44 students, not 43, had gone missing. They had been taking part in a protest over job discrimination against rural
It is not known exactly how many bodies it contains. Guerrero state prosecutor Inaky Blanco said forensic scientists were trying to identify the victims.
"We still can't talk about an exact number of bodies. We are still working at the site," Mr Blanco said at a media conference in the state capital, Chilpancingo.
At least 15 bodies have already been retrieved from the pit.
Some of the relatives of the missing students had joined the search, knocking on doors and handing out pictures of their loved ones.
State prosecutors said local officials and police officers could have links with criminal gangs operating in Guerrero state.
Arrest warrants have been issued for the mayor of Iguala, Jose Luis Albarca, and his security chief who are both considered fugitives from justice and may be involved in the violence.
Mexico correspondent Will Grant says the incident has highlighted the extent of the collusion between criminal groups and officials in much of the country.