Outraged Israeli human rights organisations have united in challenging the military's decision to invoke only minor penalties against a senior officer over the shooting of a bound and blindfolded Palestinian prisoner by a soldier under his command.

Lt-Col Omri Burberg has been "reassigned" and was indicted yesterday on the limited charge of "unworthy conduct" after the incident last month in which he held the Palestinian as the soldier shot him at close range in the foot with a rubber-coated bullet. The offence does not carry a custodial sentence.

The soldier, a staff sergeant who claims he was ordered to fire by the officer, has been demoted to private but faces the same charge. Lt-Col Burberg claimed he only wanted to intimidate the Palestinian, Ashraf Abu Rahmeh, after he was detained near Ni'ilin, the scene of regular unarmed demonstrations against the military's West Bank separation barrier.

Human rights group B'Tselem, which exposed the incident – shown on Israeli television after being videoed by a Palestinian woman in the village – said yesterday: "The army treats the shooting at point-blank range of a bound man [only] as inappropriate behaviour. It disgraces the values which it pretends to uphold."

And Yesh Din, the legal action group representing Mr Abu Rahmeh's family, pointed out that if the officer had been "caught smoking a joint" he would have suffered the worse penalty of a prison sentence and dishonourable discharge. It added: "This case proves once again that the military judicial system views harming innocent citizens as a public image problem and not as a moral issue."

Both groups have joined with the Association of Civil Rights in Israel (ACRI) in seeking to halt the court martial against the two men long enough for them to mount a high court challenge against the lightness of the indictment. In a letter to the military advocate general, Avichai Mandelblit, ACRI pointed out that the High Court ruled in 1988 that "Harming a bound and helpless person is a shameful and cruel act, and calls for an appropriately severe response".

While acknowledging that the "severe incident" reflected a "moral failure of command that should not have happened", the military said that the Chief of Staff, Gabi Ashkenazi, "recognised the positive manner" in which the officer had commanded his battalion and "commended" his actions after the incident, including his "immediate report" of it. Brigadier Mandelblit said he had taken into account "significant" penalty of reassignment, in framing the indictment.

But the lawyer acting for the victim's family, Michael Sfard, yesterday contrasted the charges with that carrying a maximum penalty of 20 years' detention of "endangering life" levelled "on a daily basis against Palestinian kids who throw stones", even if no one is hit. He added: "Of course they don't get that but they are frequently jailed for months."

Meanwhile an investigation is already underway after a later incident in which a 10-year-old boy, Ahmed Moussa, was shot dead with a live bullet after another demonstration at Ni'ilin.