Western Cape police are investigating an allegation of sex with a corpse at Salt River Mortuary, and the amputation and theft of a foot from another body.
And a reliable mortuary source said the sexual assault on a young male was "just the tip of the iceberg" and "several more young male corpses have been violated".
Two "crime against a body" cases linked to the state mortuary have been opened at Woodstock police station.
The alarm was raised after police staff at the Durham Road mortuary found that the body of a young suicide victim had been sodomised last month.
Then the foot was sawn off the body of a man who died in a southern suburbs road accident at the weekend.
It is still missing.
The investigation was launched after a policeman found a body bag unzipped and evidence of a sexual assault.
Forensic pathologists were called in and took body fluid and human tissue samples from the dead man for testing and DNA sampling.
He said that in the other case the victim's family would be contacted after police had established "beyond all reasonable doubt" that the corpse had been sodomised "post mortem".
A long-serving police officer attached to the mortuary said that in an incident in 1989 mortuary staff had caught a half-naked policeman on top of a female corpse.
He said no criminal case had been opened, but the officer had been transferred to a police station the next day.
The police watchdog, the Independent Complaints Directorate, has been told about the latest investigations but is not yet involved.
Provincial department of health spokesperson Faiza Steyn said she was deeply shocked and disgusted by the discoveries and extremely concerned for the families of the dead. "We are there to serve the community. It is a shock," she said.