Leaked documents allegedly contain evidence implicating British troops in killing children and the torture of civilians.
A BBC/Sunday Times investigation said it had obtained new evidence from inside the Iraq Historic Allegations Team (IHAT), which investigated alleged war crimes committed by British soldiers in Iraq, and Operation Northmoor, which investigated alleged war crimes in Afghanistan.
The Government closed IHAT and Operation Northmoor in 2017, after Phil Shiner, a solicitor who had taken more than 1,000 cases to IHAT, was struck off from practising law amid allegations he had paid people in Iraq to find clients.
But some former IHAT and Operation Northmoor investigators said Mr Shiner’s actions were used as an excuse to close down the inquiries.
No case investigated by IHAT or Operation Northmoor has led to a prosecution.
An IHAT detective told Panorama: “The Ministry of Defence had no intention of prosecuting any soldier of whatever rank he was unless it was absolutely necessary, and they couldn’t wriggle their way out of it.”
The year-long investigation claims to have found evidence of murders by an SAS soldier, as well as deaths in custody, beatings, torture and sexual abuse of detainees by members of the Black Watch.
A senior SAS commander was referred to prosecutors for attempting to pervert the course of justice, the investigation claims.
A Ministry of Defence (MoD) spokesman said: “Allegations that the MoD interfered with investigations or prosecution decisions relating to the conduct of UK forces in Iraq and Afghanistan are untrue.
“Throughout the process the decisions of prosecutors and the investigators have been independent of the MoD and involved external oversight and legal advice.”
The MoD said cases were referred to the independent Service Prosecuting Authority (SPA) as a result of investigations in both Iraq and Afghanistan.
“Cases from Iraq were referred as a result of historic investigations. It is untrue to claim cases investigated under Operation Northmoor in Afghanistan were not acted upon. After careful investigation, overseen by a former chief constable, no Northmoor cases were referred to prosecutors,” the spokesman said.
The MoD also said Service Police undertook extensive investigations into allegations about the conduct of UK forces in Iraq and Afghanistan, and that the SPA decided not to prosecute any of the cases referred to it.
The spokesman said: “Our military served with great courage and professionalism in Iraq and Afghanistan and we hold them to the highest standards. It is Government policy that military operations are conducted in accordance with the Law of Armed Conflict and where allegations are raised, they are investigated.
“The Sunday Times’ claims have been passed to the Service Police and the Service Prosecuting Authority who remain open to considering allegations.”