The former detainees said in an interview they were pressured to admit to crimes they did not commit.
"Our hands (were) tied and eyes covered so we couldn't see the torturers," one man said. "The informants were dictating to them that 'This guy did this, or did that'. And he was swearing to God that this guy has performed that action. But we were all innocent."
The men said they were among the hundreds of people rounded up by Iraqi security forces in October during a crackdown on Sunni fighters in northern Iraq. The two were detained at al-Muthanna until the human rights ministry gained access to the prison and closed it.
"We were tortured for four long months continuously," the other former inmate told al-Jazeera in an interview.
The local council of tribes for Nineveh province, home to most of the former detainees, held a protest Wednesday, calling on the government to respect the rule of law.
"Torture goes against human dignity. What is a man without his dignity?" Fares Abdallah al-Fares, the leader of the Nineveh tribes' council, said. "We ask the prime minister and minister of defense to apologize to the people of Nineveh."
The Iraqi Human Rights ministry said there are no secret prisons in the country.