A new investigation claims to have uncovered 54 suspicious killings by one squad during a six-month tour.
It looks at operational reports on night raids carried out by the unit in the Helmand province between 2010 and 2011 for the Panorama documentary.
The BBC claimed it found a “strikingly similar” pattern of detained Afghans being shot dead because they had pulled weapons from behind curtains or furniture.
The documentary, called “SAS Deaths Squad Exposed: A British War Crime?“, alleged there was alarm in Special Forces headquarters over these accounts.
But the Ministry of Defence hit back at the investigation hours before the documentary was due to air.
The department said it believes the investigation “jumps to unjustified conclusions from allegations that have already been fully investigated”.
“We have provided a detailed and comprehensive statement to Panorama, highlighting unequivocally how two Service Police operations carried out extensive and independent investigation into allegations about the conduct of UK forces in Afghanistan,” it said.
“Neither investigation found sufficient evidence to prosecute. Insinuating otherwise is irresponsible, incorrect and puts our brave Armed Forces personnel at risk both in the field and reputationally.”
The BBC claimed to have discovered 54 people - including two boys whose families say they were 15 and 16 - shot in suspicious circumstances during raids by the SAS unit.
It alleged there were concerns over the number of deaths during raids and the accounts among senior officers at Special Forces headquarters in London.
The documentary claims there were often many more people killed than weapons recovered, while it is usually expected to be the other way round as British troops are only meant to kill when there is an imminent threat.
SAS reports were also considered suspicious for repeatedly writing detainees were shot after grabbing weapons, as detained people are routinely searched and restrained after surrendering - meaning they should not be able to try and grab arms.
“Too many people were being killed on night raids and the explanations didn’t make sense,” a senior officer who worked at Special Forces HQ told Panorama.
“Once somebody is detained, they shouldn’t end up dead. For it to happen over and over again was causing alarm at HQ. It was clear at the time that something was wrong.”
The Ministry of Defence said it “stands open to considering any new evidence” but claimed the allegations made in the documentary had already been looked into.
“We will always investigate allegations to the full, but our independent police and prosecutors can only act on the evidence before them,” it said.
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