The Chilean navy has acknowledged for the first time that torture took place on one of its training ships shortly after the military coup in 1973.
Pinochet was president of Chile from 1974 to 1990
Navy chief Admiral Miguel Angel Vergara said his service was deeply sorry for the abuses on board the Esmeralda.
The ship became a symbol for human rights activists, and protestors often targeted it on its trips abroad.
Chile recently published its first official report on torture, which found that nearly 30,000 people were abused.
The report includes testimonies from people who said they were tortured in 1973 on the Esmeralda, Reuters news agency reported.
"Men and women were taken to the Esmeralda and from the moment of their arrest they were beaten, mistreated and threatened," the report said.
"The beatings continued on board," it added.
The report said torture victims gave testimony that they also suffered electric shocks, were threatened by fake firing squads and had their heads held under water.
After the report was published, Chile's President Ricardo Lagos said he would ask Congress to approve compensations for the victims, including payments of $190 a month.
The military police, or Carabineros, said they condemned any of their members who had been involved in human rights violations during the rule of Gen Augusto Pinochet.
Last month, the army issued a strong statement, taking full responsibility for abuses for the first time.