TIKRIT, Iraq (Reuters) - Iraqi forces backed by U.S. troops have arrested a U.S.-allied Sunni Arab militia leader, Iraqi and U.S. officials said on Sunday.

The U.S. military said Nadhim al-Jubouri, leader of a government-backed local militia and a religious leader in the town of Dhuluiya, 70 km (45 miles) north of Baghdad, and his two brothers were seized from their home on Saturday.

Derrick Cheng, a U.S. military spokesman in northern Iraq, said “members of the Iraq National Police with coalition advisors arrested three individuals. Included in the arrest was ... Mullah Nadhim Mahmud Khalil and two brothers. The National Police presented warrants ... under the charge of terrorism.”

The mostly Sunni Arab Awakening Councils, local guard units including many former insurgents who switched sides to fight al Qaeda in late 2006, have been key to cutting violence in Iraq.

As an Awakening leader, Jubouri was a key U.S. ally in the fight against al Qaeda in largely Sunni Salahuddin province, where Saddam Hussein’s hometown is located.

Ahmed Karim, the deputy governor of Salahuddin province, said Jubouri was accused in killings that took place in the largely Shi’ite town of Dujail during the height of Iraq’s sectarian conflict in 2006-2007.

“People from Dujail brought charges against Mullah Nadhim for the murder of their relatives,” Karim said.

He said that at the time the alleged crimes took place, Jubouri was an al Qaeda operative. Karim’s account of the charges facing Jubouri could not be immediately confirmed.

Prime Minister Nuri al-Maliki said Jubouri should be released if he had been detained on an old warrant. “This man was with al Qaeda and he entered the political process. It seems that there was an old warrant that was acted on now, ” he said.

He said the situation was under review.

The Awakening militias were backed and paid by U.S. forces until the Iraqi government took control of them in recent months. Since then, payment of their salaries has fallen far behind schedule.

Many regard the Shi’ite-led government with suspicion and have been dismayed by salary delays, attacks on guard units, and a spate arrests of guards in recent months.

In late March, Iraqi forces seized Adil al-Mashhadani, head of a patrol unit in central Baghdad’s Fadhil neighborhood, sparking clashes with his supporters that killed three people.

Several others have been detained. U.S. and Iraqi officials deny the government is targeting the guards because of their sect or insurgent past, but say those who have committed grave crimes must face justice.

Guards have come under attack, and at least 125 have been killed since October, U.S. officials say. On Saturday, gunmen opened fire at a guard unit south of Baghdad, wounding one.