* Sunni militants and security force fought over prison
* Police say prisoners were collateral damage
* Sunni mayor and governor say they were executed
By Oliver Holmes
BAGHDAD, June 19 (Reuters) - The boy was shot in the head twice. His family say he was imprisoned for using an unregistered SIM card. But the next time they saw him was at the morgue - one of 52 dead prisoners mostly with execution-style wounds to the head and chest.
The world has been shocked this week by video footage of Sunni militants from the Islamic State of Iraq and the Levant gunning down scores of prisoners piled in a shallow grave during their lightning advance through northern Iraq.
But Sunni residents say government forces and their allied Shi'ite militia are responsible for similar atrocities, pointing to the deaths of dozens of prisoners at a jail in Baquba, a provincial capital in a religiously-mixed area an hour north of Baghdad that came under insurgent attack on Monday night.
The government says the prisoners were all killed in a crossfire when the jail came under attack. But local Sunni officials, including the governor and the mayor, say the prisoners were executed by their guards. The only surviving prisoner was later kidnapped and murdered, leaving no witnesses.
According to the local chief of police, ISIL fighters tried to assault the jail in the Mafraq district of Baquba, capital of Diyala province, during an attempt to seize the town on Monday.
The battle raged throughout the night and eventually ISIL was pushed back. In the morning the 52 prisoners were found dead.
Residents say the prisoners at the jail were mostly being held for petty crimes. The police say they were terrorism suspects.
Staff Brigadier General Jameel al Shimmeri, the local police chief, said that ISIL fighters used mortar bombs and grenades in the fighting and that the prisoners were killed by stray gunfire and from explosions nearby.
"After the battle cleared, we had one security forces member killed and found the prisoners had also been killed," he told Reuters. "It's a small prison, a house in the middle of a residential area, and it wasn't heavily fortified. The prison was like a battlefield and it was highly likely the prisoners would be exposed to gunfire just like any of us," he said.
But Sunni officials say the bodies showed that the victims had been gunned down, not accidentally hit by stray fire. The mayor of Baquba, Abdullah al-Hyali, said he visited the morgue and saw most of the victims had bullet wounds to the head.
One of the victims was his nephew who had been shot twice in the head.
"He was severely tortured and his nails were extracted," the mayor told Reuters.
Bassim al-Sammarai, spokesman for Diyala's governor Amer al-Mujamaii, said he too had seen the bodies and most of them had bullet wounds to the head.
An employee of the morgue and a police officer, both of whom spoke on condition they not be identified, also said most victims had been shot in the head or chest, execution style.
The mayor and governor tried to visit the prison the day after the fighting, but say they were prevented by around 50 plain-clothes militiamen from reaching the building.
"They pointed their guns at us and we were forced to go back to the cars," the mayor said. "We didn't see any marks of mortar rounds as claimed by the police chief on the outer fence."
His nephew's body also had a 9 mm pistol bullet casing in his clothes, indicating shots were fired from inside the prison, the mayor added.
Baquba and its surrounding districts have long been among the most violent parts of Iraq, where Sunnis and Shi'ites live in neighbouring villages and have accused each other of regularly committing atrocities since the days of U.S. occupation.
Sunnis say they are targeted by Shi'ite militia and security forces. Shi'ites are regularly attacked by insurgent gunmen and suicide bombers.
The governor's spokesman, Sammarai, said the lone survivor from the prison was a man called Ahmed Zaidan al-Harbi.
"He survived but suffered from injuries to the head and chest. He told the governor that the prisoners had suddenly come under gunfire. He was too weak to talk so we left shortly afterwards," Samarrai said by telephone.
"Later we were told he had been kidnapped from the hospital. And we are still investigating the matter. We don't have any evidence on who was behind it."
Harbi's lifeless body was dropped off at the morgue on Thursday morning. (Editing by Peter Graff)