A single American Special Forces group was behind at least three of Afghanistan's worst civilian casualty incidents, The Independent has learnt, raising fundamental questions about their ongoing role in the conflict.

Troops from the US Marines Corps' Special Operations Command, or MarSOC, were responsible for calling in air strikes in Bala Boluk, in Farah, last week – believed to have killed more than 140 men, women and children – as well as two other incidents in 2007 and 2008. News of MarSOC's involvement in the three incidents comes just days after a Special Forces expert, Lieutenant-General Stanley McChrystal, was named to take over as the top commander of US and Nato troops in Afghanistan. His surprise appointment has prompted speculation that commando counterinsurgency missions will increase in the battle to beat the Taliban.

MarSOC was created three years ago on the express orders of Donald Rumsfeld, US defence secretary at the time, despite opposition from within the Marine Corps and the wider Special Forces community. An article in the Marine Corps Times described the MarSOC troops as "cowboys" who brought shame on the corps.

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The first controversial incident involving the unit happened just three weeks into its first deployment to Afghanistan on 4 March 2007. Speeding away from a suicide bomb attack close to the Pakistan border, around 120 men from Fox Company opened fire on civilians near Jalalabad, in Nangahar province. The Marines said they were shot at after the explosion; eyewitnesses said the Americans fired indiscriminately at pedestrians and civilian cars, killing at least 19 people.

The US Army commander in Nangahar at the time, Colonel John Nicholson, said he was "deeply ashamed" and described the incident as "a stain on our honour". The Marines' tour was cut short after a second incident on 9 March in which they allegedly rolled a car and fired on traffic again, and they were flown out of Afghanistan a few weeks later.

The top Special Operations officer at US Central Command, Army Major General Frank Kearney, refuted MarSOC's claims that they had been shot at. "We found no brass that we can confirm that small-arms fire came at them," he said, referring to ammunition casings. "We have testimony from Marines that is in conflict with unanimous testimony from civilians."

At the military hearings on the incident, which were held back in the US, soldiers said the MarSOC troops, who called themselves Taskforce Violence, were gung-ho and hungry to prove themselves in battle. The inquiry also heard testimony suggesting there were tensions between the Marine unit and its US Army counterparts in Nangahar province.

Col Nicholson told the court the unit would routinely stray into areas under his control without telling him, ignoring usual military courtesies. "There had been potentially 25 operations in my area of operations that I, as a commander, was not aware of," he said. Asked about the moment he was told of the March shootout, he added: "My initial reaction was, 'What are they doing out there?' " The three-week military inquiry ultimately spared the Marine unit from criminal charges.

There are around 2,500 troops in MarSOC. Around half are frontline troops, the rest are support and maintenance. Originally the unit was used to plug gaps in the Special Forces world and it has operated in more than 16 countries since being set up by Mr Rumsfeld in 2006. However, in a recent interview, its commanding officer, Major General Mastin Robeson, revealed he has been ordered to focus on Afghanistan and Pakistan. Today MarSOC answers to the Combined Forces Special Operations Component Command, based in Kabul. That in turn answers to US Forces Afghanistan, which is led by the top US commander, David McKiernan, who is soon to be replaced by General McChrystal.

In August last year, a 20-man MarSOC unit, fighting alongside Afghan commandos, directed fire from unmanned drones, attack helicopters and a cannon-armed Spectre gunship into compounds in Azizabad, in Herat province, leaving more than 90 people dead – many of them children.

And just last week, MarSOC troops called in the Bala Baluk air strikes to rescue an Afghan police patrol that had been ambushed in countryside in Farah province. US officials said two F18 fighter jets and a B1 bomber had swooped because men on the ground were overwhelmed. But villagers said the most devastating bombs were dropped on compounds some distance from the fighting, long after the battle was over, and when Taliban forces were retreating. Afghan officials said up to 147 people were killed, including more than 90 women and children.

US officials dispute the number of people killed in each of the MarSOC incidents, which sparked angry public demonstrations and condemnation from Afghan President Hamid Karzai.

The spokesman for US forces in Afghanistan, Colonel Greg Julian, denied reports that commanders have lost confidence in the Marine unit. "MarSOC was involved in these incidents, but it's not all the same guys. They get the lessons passed on from all of the rotations and experiences. Yet, they are human," he said. "They have the same rules of engagement that everyone has."

The so-called "tactical directive" was introduced last September in the wake of the international uproar that followed the Azizabad deaths. It requires troops to exercise "proportionality, restraint, and utmost discrimination" when calling in air strikes. Claims that bombs were dropped in last week's incident in Farah long after the fighting finished suggest those directives may not have been followed by MarSOC.

Meanwhile, Afghan MPs have called for new laws to regulate the presence of foreign forces in Afghanistan, and limit use of air strikes, house searches and Special Forces operations. Sayed Hussein Alemi Balkhi, one of the chief proponents of the planned legislation, said: "Special Forces, all forces, should be regulated by the law. If they won't accept that we have to ask bigger questions about what they are doing here."