A teenage Palestinian killed by a senior Israeli army officer last week was shot in the back and side while apparently fleeing, according to medical evidence and multiple Palestinian witness reports.

Mohammed Kasbeh, 17, was among a group of stone-throwers near a major Ramallah checkpoint when they broke the windscreen of a passing brigade commander’s car with a rock. He died after being shot several times in his upper body by the officer.

After shooting Mohammed, the officer allegedly kicked the dying teenager on the ground before leaving the scene.

The killing of Mohammed near the Qalandia checkpoint last Friday received widespread coverage in the Israeli media, both because of the seniority of the officer involved – a brigade commander, Col Yisrael Shomer, and because of the support he received immediately after the shooting from senior members of Israel’s government, including education minister Naftali Bennett.

Palestinian men walk next to the Israeli West Bank separation barrier near the Qalandia checkpoint, where the shooting took place. Photograph: Alaa Badarneh/EPA

The killing was given extra prominence because two of Mohammed’s brothers – aged 15 and 11 – were also killed by the Israeli military during the second intifada, while a third brother survived being shot.

The incident occurred in the early morning when an Israeli vehicle in which Shomer was travelling with other soldiers drove along a section of road between the Palestinian neighbourhood of al-Ram and the Qalandia checkpoint towards a gate in the separation wall used by the Israeli military.

What appears not to be in dispute is that at a roundabout close to the Qalandia checkpoint a group of youths threw stones at the vehicle, breaking its windscreen. It is what happened next that is at the centre of the disputed claims.

According to the first account of the Israeli military, under a hail of rocks Shomer exited the car and – fearing for his life – shot and killed one of the group amid continued stone-throwing.

Multiple Palestinian eyewitnesses, however, tell another story. They claim that the Israeli car pulled over by the side of the road and two or three soldiers exited, chased the fleeing youths for a few metres before Shomer paused, took aim and shot Mohammed several times as he ran away – claims that seem consistent with the medical examination of his body.

As Mohammed lay dying, say witnesses, Shomer approached him and kicked or pushed him with his foot before leaving and driving away.

None of the officers in the car suffered any injuries.

A medical report – obtained by the Guardian – supported by an interview with the doctor who examined Mohammed when his body was admitted to hospital – describes how he was shot in the back and obliquely in the side of the head – not front on – with the most serious injury a gunshot wound penetrating his upper left back. A second bullet entered his mouth – also from the side – becoming lodged in his jaw.

A description of the fatal shooting by two Palestinian witnesses interviewed by the Guardian suggests – if these accounts are accurate – the Israeli soldiers involved were in breach of the military’s own recommendations over the use of live ammunition in attempted arrests – appropriate for a fleeing individual – firing at the upper body, not the legs.

Fadi Ziad was working at a petrol station about 30 metres from where Mohammed was shot. “It was around 6.30 in the morning,” Ziad told the Guardian. “There were three young guys at the roundabout who were throwing rocks. A jeep came past – not one of the ordinary ones but one the officers use – and they threw rocks at it.”

An IDF statement said: ‘Military police investigations are automatically opened into all incidents resulting in death in the West Bank.’ Photograph: Björn Kietzmann/Demotix/Corbis

According to Ziad, the soldiers pulled over their car and stopped on the opposite side of the road to where he was watching.

“They got out. There were two with helmets and a soldier without a helmet.” He said the soldier without a helmet appeared to be older.

“They started chasing the youths. The one who was shot was moving with his back towards them but with his head turned towards where they were. He was running away sideways on. The soldiers were 10 to 15 metres from the youths when they shot the one who died. After he fell on the ground the soldier without the helmet went and checked him and kicked him.”

At Mohammed’s funeral on Friday, his grief-stricken friend Ahmad Tahir – one of the youths present throwing stones – recounted an identical story. “He was running away,” he said. He also said that after the shooting one of the soldiers kicked the prone teenager.

Among those who defended Shomer’s action on the basis of what was known at the time was Bennett, who wrote on his Facebook page: “I completely stand behind the Binyamin Brigade commander that acted facing a terrorist to defend his own life and the lives of his soldiers. This is how a commander in the IDF should act. The people of Israel are behind you.”

Shomer’s action was also defended by the deputy defence minister, Eli Ben Dahan, and his own commanding officer despite the fact that an ongoing military police investigation was opened into the killing.

The human rights group B’Tselem – which conducted its own investigation into the killing – said on Tuesday that its investigation had heard exactly the same evidence from three witnesses separate from the ones interviewed by the Guardian.

The B’Tselem witnesses only differ from Fadi Ziad’s account in saying it was two not three soldiers who left the vehicle.

“We spoke to Haroun Hazim, another of the youths there with Mohammed,” said Itamar Barak, a researcher with the group. “He said they were at the roundabout when someone shouted that a military vehicle was approaching.

“Then a stone was thrown. The vehicle stopped immediately and he says he people exited the car, the driver and the high-ranking officer.

“The officer ran a few metres and the youths ran and tried to hide but Kasbeh was quite visible. The officer then set himself in position and fired several shots and then came and kicked him.”

Two other witnesses, drivers from Jenin who were parked nearby, also gave the group the same account, saying after Mohammed was shot the officer “checked the body with his foot”.

Sarit Michaeli of B’Tselem added: “The central issue for us is that this action by the highest-ranking officer in the region – backed up by military commanders – suggests that the disproportionate use of force won’t be sanctioned but will condoned. And that s is very dangerous.

The Israel Defence Forces declined to answer any specific questions relating to the incident but released the following general statement: “The commander and his forces, who were on their way to Qalandiya crossing, were attacked by a number of Palestinians hurling stones at their vehicle at close range. The commander, fearing a lynch that would place his subordinates and himself mortal danger, exited his vehicle and implemented standard procedure for the apprehension of suspects. Military police investigations are automatically opened into all incidents resulting in death in the West Bank.”