An independent review of Crown Office and Procurator Fiscal Service (Copfs) procedures found that in three cases the brains of deceased persons were kept to help the investigation into their deaths.
The bodies were released but relatives were not told the brain had been retained by the pathology department.
The failure to notify the families was due to an "oversight" by those dealing with the death at the local procurator-fiscal's office, the report says.
In three more cases, brains were kept for specialist neuropathology examination after the deaths resulted in criminal proceedings and, ultimately, convictions for murder.
Relatives were not told because the retention of the brain was noted in the initial death report but not in the criminal files.
A further 10 cases were found where relatives were told an organ had been kept but were not asked what should happen once it was no longer required.
The Inspectorate of Prosecution in Scotland was commissioned to review why Copfs systems failed in each case.
The inspectorate has made 10 recommendations, including that the Copfs should publish annual figures of the number of organs retained.