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.
The six cases, which took place between 2007 and 2012, were identified in a national audit ordered by the Lord Advocate.
A further 10 cases were found where relatives were told an organ had been kept but were not asked their views on what should happen once it was no longer required.
The Inspectorate of Prosecution in Scotland (ISP) was commissioned to review why COPFS systems failed in each case.
Its report concluded: "The systematic failures that led to nearest relatives not being informed that an organ had been retained were two-fold.
"The first was a failure to adhere to COPFS procedures as a result of an oversight by those dealing with the death in local procurator fiscal offices.
"The second arose due to a lack of clarity, following the creation of specialist homicide teams, on whether it was the responsibility of the team investigating the criminal aspect of the death or those, to whom the death was initially reported, to liaise with the nearest relatives."
The inspectorate has made 10 recommendations, including that the COPFS should publish annual figures of the number of organs retained.
HM Chief Inspector Michelle Macleod said: "The public must have confidence that the examination of a body after death is conducted in a respectful manner and the nearest relatives are informed of all important decisions, including if an organ or significant body part has to be retained and of the reasons for retention.
"We make 10 recommendations designed to provide assurance that the procedures implemented by COPFS are professional, effective, sensitive and that there are sufficient safeguards to prevent any further instances of nearest relatives not being informed of organ retention following a post-mortem authorised by the procurator fiscal.
"We are pleased that COPFS has accepted all of the recommendations and has commenced implementation of those that relate solely to COPFS."
Further audits of the procedures governing organ retention will be carried out in six and 12 months' time, she added.
The COPFS said it receives reports of around 12,000 deaths a year, and in "a very small number" of cases, pathologists advise that they need to retain an organ for further scientific examination, due to the complexity of investigations into an unexplained death.
A statement said: "COPFS appreciates that the public will wish to be assured that processes are in place so that families affected by this requirement are aware of the position. Accordingly we will publish information to confirm the small numbers of cases where this has occurred annually.
"As at 30th June 2014 there are only six cases in which organs have been retained. The family in each case has been advised of the position by the procurator fiscal and made aware of the reason for the retention."