Iraq's Interior Ministry has charged 57 employees, including top level security force members, with human rights abuses at a secret prison uncovered in May.
Iraqi and US officials found the jail at a building in east Baghdad belonging to the Shia-Muslim dominated ministry.
More than 1,400 mainly Sunni prisoners were being held, many showing signs of physical and psychological abuse.
The prison was known as Site Four. It was alleged to have been run by Shia militia members within Iraq's police.
Former interior minister Bayan Jabr denied allegations of systematic human rights abuses.
But his successor, Jawad Bolani, has sacked thousands of employees, and last month suspended an entire police brigade that had been accused of links to death squads.
BBC Middle East analyst Roger Hardy says repeated accusations of abuses have embarrassed not just Iraq's Shia-dominated government but also the Americans.
Washington has been urging Prime Minister Nouri Maliki to take firmer action.
One question that remains unanswered is whether the government will act against Bayan Jabr, our analyst says.
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