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By Hannah O'Grady and Joel Gunter
BBC Panorama
Veterans Minister Johnny Mercer raised serious concerns in government in 2019 over the decision to close an investigation into UK special forces.
The BBC understands that Mr Mercer wrote to then-defence secretary Ben Wallace to warn against the closure.
The veterans minister, a former British army officer, was privately concerned that there were credible war crimes allegations against British forces.
When the closure was later announced, Mr Mercer publicly backed the decision.
The investigation, known as Operation Northmoor, had set out in 2014 to investigate a total of 675 allegations of wrongdoing by UK armed forces in Afghanistan.
They included allegations that the nation's elite special forces regiment, the SAS, had murdered dozens of unarmed men, detainees, and civilians during raids.
But Operation Northmoor, which was being conducted by the Royal Military Police, was shut down in 2019 with no charges.
Minister 'warned colleagues'
In 2022, the government announced a public inquiry into the allegations, after BBC One's Panorama revealed that one SAS squadron had killed 54 people in suspicious circumstances in one six-month tour of Afghanistan.
The decision to wind down and then close Operation Northmoor with no charges caused consternation among some members of the government and civil service.
The BBC understands that Mr Mercer, who served as an Army officer in Afghanistan and had worked alongside UK special forces there, was concerned SAS units may have broken the law during operations, shooting dead unarmed people and planted weapons beside their bodies to justify the killings.
There is no suggestion that Mr Mercer had been a direct witness to or had first-hand knowledge of war crimes.
The veterans minister warned colleagues that the government could suffer more reputational damage in the long run if it did not seriously investigate alleged British war crimes and prosecute if necessary.
An internal email disclosed as part of a subsequent legal case against the Ministry of Defence suggests that Mr Mercer believed the government should publicly acknowledge that "things went wrong on such operations in Afghanistan".
In the email, the deputy head of the MoD's legal department, writing in late 2019, recounts dissuading the veterans minister that such a statement should be made, on the basis that it could prejudice a review of Operation Northmoor that was being considered by a High Court judge.
As a serving government minister, Mr Mercer publicly backed the decision to close both Operation Northmoor and a similar investigation into operations in Iraq, known as IHAT. The closures of both investigations followed allegations that a lawyer, who had taken more than 1,000 cases to IHAT, had paid local intermediaries in Iraq to find claimants.
'Flawed' investigations
Mr Mercer told the Sunday Telegraph that the closure of Northmoor was "another significant moment as we retake ground ceded over the years to those who seek to rewrite history and line their own pockets with no regard at all for the damage they have done to some of our nation's finest people".
Speaking during a debate in Parliament a few months earlier, he told the House of Commons that "the allegation that our armed forces operated so-called death squads in Afghanistan" was "simply not true".
Speaking more broadly about UK operations in Afghanistan and Iraq, in the same parliamentary debate, Mr Mercer said it was a "matter of deep personal regret that original RMP investigations were flawed and that opportunities to hold those responsible to account may now have been lost".
"For this, I unreservedly apologise to those who suffered treatment at the hands of UK forces that was simply unacceptable," he said.
When approached for comment, Mr Mercer told the BBC: "Given the ongoing Independent Inquiry relating to Afghanistan it would be inappropriate to comment on this matter."
Operation Northmoor has faced criticism in the years since it was closed over an apparent failure to interview key witnesses or secure vital evidence relating to allegations of extra-judicial killings.
Officers from the Royal Military Police, which was responsible for the investigation, told Panorama they were blocked by senior military figures from interviewing special forces officers and accessing forensic evidence.
They said Operation Northmoor was closed before military police could complete their investigation.
An MoD spokesperson told the BBC that it was not appropriate for them to comment on allegations which may fall into the scope of the public inquiry.
The public inquiry will begin hearing evidence on Monday.
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