The Israeli military says an officer filmed ordering a soldier to shoot a bound and blindfolded Palestinian prisoner has resigned his command of an army battalion but will continue to serve elsewhere.

A military statement said Lieutenant Colonel Omri Borberg asked to be removed from his post following the July 7 incident on the outskirts of the West Bank village of Naalin when a soldier shot a captured Palestinian demonstrator in the foot with a rubber-coated bullet from close range. The shooting was captured on video by a local resident and distributed by an Israeli human rights group.

The images show Borberg holding Ashraf Abu Rahmeh by the arm while a soldier, who has not been named, takes aim and fires at the prisoner's foot. Abu Rahmeh suffered a bruised toe.

He was one of several dozen Palestinians who hurled stones at soldiers during a protest against Israel's separation barrier, which is under construction near Naalin and will eventually cut off the village from hundreds of hectares of its land.

The military said that Borberg and the soldier were charged in a military court for inappropriate conduct. No date was set for trial.

Local media reports said the charge was a minor one for which the men, if convicted, would serve no jail time and carry no criminal record.

Human rights group B'Tselem, which publicised the video, issued a statement deploring the military's decision not to press criminal charges.

"An army that treats the shooting of a bound detainee, from zero range as "inappropriate conduct" is disgracing the values it claims to hold," B'Tselem wrote.