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Brig. Gen. Saad Maan Ibrahim, the Interior Ministry spokesman, put the death toll at 36, including six police officers and 30 prisoners, and said 40 inmates escaped.
Ibrahim told The Associated Press that a fight broke out among the inmates of the prison and when guards went to investigate, they were overpowered and had their weapons taken. Some of those who escaped were wanted on terrorism charges, Ibrahim added. He said security forces had cordoned off the area and were hunting for the escaped inmates.
The town of Khalis is located about 50 miles north of Baghdad.
In a statement carried on militant websites, the local chapter of the Islamic State group claimed a completely different account of the incident, describing it as a coordinated operation involving the use of multiple explosives outside the prison. The statement claimed that 30 Islamic State members were among those who escaped.
Ibrahim had originally denied there was any external force involved and he did not immediately respond to requests for comment on the militants' version of events.