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In this Tuesday, Oct. 30, 2012 photo, a Syrian rebel takes a break during fierce fighting in the town of Harem in Idlib province, Syria.Mustafa Karali/The Associated Press

Unarmed and cornered by Syrian rebel fighters, the man seemed to accept his death with more silent sorrow than surprise; his killers did not hesitate as they shot their prisoner.

The incident, filmed by a Reuters video crew, happened last week in Harem, near Aleppo, where rebels have surrounded hundreds of troops and militiamen loyal to President Bashar al-Assad. Taking one neighbourhood after days of bitter street fighting, opposition fighters went from house to house.

From one building they hauled a man in middle age, dressed in casual clothes, black bearded and without a weapon. He seemed anxious and shied away as he stumbled into the street. Three rebels fighters casually raised their Kalashnikov rifles. A shot rang out, then another. A third. The man began to fall. Still silent. More shots. He lay still. A final round hit his head.

For rebel commanders who present their siege of the former Crusader fortress town of Harem as a showcase for efforts to forge a disciplined fighting force out of motley volunteers, the killing was an embarrassment, offering evidence that Assad's "shabbiha" gunmen have no monopoly on atrocities.

Brigade commander Basel Eissa did shout at his men but was unable to stop them. Leaders of the unit said the fighters were angry at taking casualties. They also justified their action by saying they later found documents showing the dead man was a loyalist army officer – though that would be no defence in a war crimes court.

"I try to remind them that there are moral reasons we do not just kill soldiers," Eissa said. "And beyond that, I tell them that strategically it is bad – we get help or information when we spare these men's lives. We are not their judge; God is."

Commanders are also aware that bad publicity could hamper rebel efforts to secure arms and funding from abroad that might allow them to better match the tanks, aircraft and artillery which Assad's forces are using against them to deadly effect.

Eissa himself was killed in an air strike earlier this week.

Investigators accuse pro-government forces of war crimes, including the murder and torture of civilians, in what they said in August may be a state-directed policy. They said rebel fighters were also guilty of war crimes, including executing prisoners, but on a smaller scale.

Assad's state media give extensive coverage to allegations of atrocities committed by opponents, whom the president brands as "terrorists" bent on destroying Syrian society.

Major Mohammed al-Ali, an army defector at Harem trying to coordinate rebel brigades in the hope of greater international support, said: "In every battle, there are violations. We deal with them harshly to make an example of them."

There was no sign of immediate punishment, however, for those fighters who killed the prisoner last week, although their commanders in the field reprimanded them. After the shooting, the unit involved continued its operation.

Elsewhere in Harem, journalists saw the bodies of four uniformed soldiers lined up in a garden, all shot in the head. And, although dozens of prisoners were held by rebels at Harem, at least one fighter there described commanders' calls for fair treatment as a smokescreen to keep the killing hidden.

More and more instances of executions are coming to light, including a video uploaded to the Internet last week that showed rebels in another part of Idlib province in the northwest lining several soldiers up against a wall and gunning them down, an act the United Nations has said could constitute a war crime.

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