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