The Los Angeles Times reported Iraqi officials as saying that more than 100 prisoners had been tortured with electric shocks, suffocated with plastic bags or beaten.
'Human rights abuses'
UK-based human rights group Amnesty International urged Nouri al-Maliki, the Iraqi prime minister, to investigate the allegations of abuses against the predominantly Sunni detainees.
"We found judges and representatives of the public prosecutor installed inside the prison, which means the prison is not a secret one"
Kamil Amin, spokesman for Iraq's human rights ministry
"The existence of secret jails indicates that military units in Iraq are allowed to commit human rights abuses unchecked," Hassiba Hadj Sahraoui, Amnesty's Middle East and North Africa deputy director, said in a statement on Monday.
Maliki, who is looking to build a parliamentary majority following elections last month, has denied any knowledge of the prison, but Amnesty said that this did not absolve the government of responsibility.
"Prime Minister Maliki's claim that he was unaware of abuses cannot exonerate the authorities from their responsibilities and their duty to ensure the safety of detainees," Sahraoui said.
"Maliki's government has repeatedly pledged to investigate incidents of torture and other serious human rights abuses by the Iraqi security forces, but no outcome of such investigations has ever been made public."
Prison 'not secret'
Amin rejected the description of the facility, by the Los Angeles Times and Amnesty, as a "secret prison".
"We found judges and representatives of the public prosecutor installed inside the prison, which means the prison is not a secret one," he said.
Amin said his ministry had collected enough evidence to prove that the prisoners, who were detained during an operation in October targeting alleged Sunni fighters in Nineveh province, were transferred from Nineveh to Baghdad legally.
But Atheel al-Nujaifi, the governor of Nineveh, contested Amin's claims.
"The prisoners were transferred without court or investigation judge orders," he said.
Al-Nujaifi accused the security forces of targeting civilians in his province.
The whereabouts of the detainees came to light in March after relatives of the missing men raised their concerns with Iraq's human rights ministry.