Family members of Gonzalo Montoya Jiménez said he already had “autopsy marks on him” ahead of the planned procedure.
Jiménez, jailed in Spain’s Asturias region, is thought to have suffered catalepsy.
The condition causes a person’s vital signs to slow down until they are nearly imperceptible.
He had been bagged-up and taken to the Institute of Legal Medicine in the region’s capital Oviedo on Sunday morning.
Police guards had found him slumped and unconscious at Asturias Central Penitentiary in Villabona.
The inmate is reported to have awoken just three hours before the planned post-mortem examination.
Newspaper La Voz de Asturias said it was not immediately clear what crime Jiménez was jailed for or what length his sentence is.
A Spanish Prison Service spokeswoman confirmed the prisoner’s family were told he had died.
She said: “Two prisoner doctors concluded he had clinical signs of death following a morning roll call and informed police, his next-of-kin and a local duty court as part of standard procedure.
“The court sent a forensic doctor who was the one who confirmed his death.
“I can’t comment on what happened at the Institute of Legal Medicine but three doctors have seen clinical signs of death so it’s still not clear at the moment exactly why this occurred.”
His family are said to believe only one doctor saw his body before two others signed a death certificate without seeing the report.
Jiménez’s family also told local media that the prisoner has epilepsy and this may have contributed to his unusual case.
His body was taken to a hospital Oviedo where he is now in intensive care.
Civil Guard Officers have been tasked with keeping watch on the resurrected prisoner while he is treated in hospital.
A police source said: “We got the original call asking us to attend the jail because and inmate had died and acted according to protocol.
“He was taken away for an autopsy without police presence because at that point he was thought to be dead.
“The second call that came in asking for police assistance in taking him to hospital and keeping watch over him while he was there for obvious security reasons obviously came as a bit of surprise.”