Witnesses said the authorities dug up the mass grave at Casablanca's main fire station on Saturday night and reburied the remains in separate graves on a nearby lot, angering relatives and rights activists.
The excavation of the grave, part of a drive to lift the lid on past rights abuses, and the reburial of the remains may have tampered with evidence needed to prosecute those who carried out the killings, families and activists said on Monday.
Reports of the operation appeared in newspapers on Monday.
The dead were among about 1000 people killed by police in anti-government riots in Casablanca on 20 June, 1981, when crowds protested against food price rises, according to human rights groups.
Families and rights activists were kept away from the grave and reburial sites. A plainclothes policeman told a reporter: "Move out here! We do not want people here and the parents of the dead to come here and make trouble."
A security source near the scene told Reuters: "About 100 bodies were found and reburied."
"Move out here! We do not want people here and the parents of the dead to come here and make trouble"
Human rights groups said the government buried the dead in at least seven mass graves scattered across the city.
The discovery is part of a truth-seeking process in Morocco after the reform-minded King Mohammed ordered the independent Equity and Reconciliation Commission last year to investigate human rights abuses.
The abuses during the rule of the late King Hassan took place over a period of more than 40 years until 1999. This period was known as the "years of lead" when many dissidents and coup plotters were killed, tortured and abducted.
The commission formally ended its investigations and submitted a report to Mohammed last month. Its findings have not yet been made public.
Three non-governmental human rights organisations and a group uniting families of the dead criticised the authorities for their treatment of the bodies in the mass grave.
In a joint statement they said: "We consider the way the authorities handled the digging up of the mass grave and the removal of the remains will tamper with the evidence and damage the remains of the dead.
"We demand the prosecution of those responsible for the crime of killing our loved sons and daughters, buried in that mass grave. We consider this a crime against humanity."