BAGHDAD—The quarrel didn’t last long.

Angry Sunni fighters temporarily abandoned their checkpoints in a western Baghdad neighborhood after Iraqi soldiers briefly detained some of their colleagues, whose U.S.-backed patrols have helped curb violence.

The dispute last weekend, although relatively minor, points to a deeper and more complex test next Wednesday as the Shiite-led government begins to assume authority over the Sunni fighters, also known as Sons of Iraq.

Many of the fighters are former insurgents and suspect their new masters want retaliation rather than reconciliation. Much of Iraq’s ceaseless violence in 2006-2007 was sectarian-based, with Sunnis and Shiites launching horrific attacks on each other.

Prime Minister Nouri al-Maliki has vowed to reward those who joined in the fight against al-Qaida in Iraq, which lost most of its Sunni strongholds when local tribesmen turned against the extremist group and joined the U.S. payroll. The U.S. considers the initiative a test of the government’s willingness to reconcile with Sunnis.

But tens of thousands of mostly Sunni neighborhood guards—a key element in the sharp drop in attacks in Iraq since last year—are deeply uneasy about the Iraqi government. Some Sons of Iraq groups, also labeled Awakening Councils, have complained about arrests and harassment by police and soldiers.

“They want to occupy checkpoints instead of us,” said Wahab al-Zubaie, an Awakening Council spokesman in the western Baghdad district of Abu Ghraib, where the weekend dispute took place in the neighborhood of al-Hamdaniya.

Al-Zubaie warned that security could deteriorate if Sunni fighters are sidelined because they know “movements of al-Qaida members and their whereabouts” better than government forces do.

Last week, an angry Salah al-Ageidi, the Awakening Council leader in the primarily Sunni neighborhood of Dora in southern Baghdad, accused Iraqi police of detaining and beating up several of his 850 men before letting them go.

“We want to protect our area and we have succeeded in this so far,” he said. “If we are disbanded, then chaos will prevail again in Dora.”

Lt. Gen. Lloyd Austin, the No. 2 U.S. commander in Iraq, has said the Iraqi government will begin paying the salaries of about 54,000 mostly Sunni fighters in Baghdad province. Monthly income is expected to be about $300, the same amount that the Americans are paying. There are nearly 100,000 Awakening Council members altogether.

Iraq plans to merge 20 percent of the Awakening Council members into the security forces, while others could obtain jobs in civilian ministries or rebuilding and repairing damage from the war. The question is whether enough Awakening Council members will get the work and money to prevent them drifting into alienation, and even outright defiance toward the government.

“There are frictions in any transition. We should not expect this one to be any different,” said U.S. Brig. Gen. Robin Swan, deputy commanding general of the 4th Infantry Division.

Swan spoke in an armored vehicle as it lumbered through Mansour, a mostly Sunni, western neighborhood of Baghdad that once hosted elite loyalists of Saddam Hussein and his Baath party. The upscale area sank into chaos after the U.S.-led invasion in 2003, but Awakening Councils have helped restore some peace.