Calls for an independent inquiry are mounting after the UK Government and the army were accused of covering up the killing of civilians in Iraq and Afghanistan.

An investigation by BBC Panorama and the Sunday Times has uncovered claims of torture, abuse, sexual humiliation and murder – including the killing of children – at the hands of British soldiers, including members of Scottish battalion the Black Watch.

Leaked documents from 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, are said to contain evidence of the abuse.

The Government decided to close down the operations in 2017 after a lawyer who had taken more than 1,000 cases to IHAT was struck off following allegations he had paid fixers in Iraq to find clients.

Former detectives from the investigation units told The Sunday Times this was just an excuse to close down criminal investigations. None of the cases investigated by IHAT or Operation Northmoor resulted in a prosecution.

However, the Ministry of Defence (MoD) said it rejected the unsubstantiated allegation of a pattern of cover-ups.

The claims were described as “deeply chilling” by SNP defence spokesman Stewart McDonald.

“What is outlined in these reports represent gross violations of the Geneva Convention and attempts to cover-up crimes of the worst possible kind,” he said. “This cannot be taken lightly and must not be swept under the carpet.

“It may be the case that the International Criminal Court has a role to play in establishing the truth. There is clear public interest in an independent inquiry, led by a judge, being established and it must be free of any kind of political interference.”

Amnesty International Scotland said soldiers who break the law must face the consequences.

Naomi McAuliffe, of Amnesty International Scotland, said: “The allegations in the Sunday Times investigation are extremely disturbing. UK military personnel serving overseas should not inflict torture or other human rights abuses in the course of their duty.

“All victims of human rights violations – regardless of whether they were committed in the midst of conflict – have the right to an independent investigation and for the results to be published followed by full accountability.”

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.

An IHAT detective told Panorama: “The Ministry of Defence had no intention of prosecuting any soldier, whatever rank he was, unless it was absolutely necessary and they couldn’t wriggle their way out of it.”

The MoD said military operations were conducted according to the law and there had been an extensive investigation.

“Investigations and decisions to prosecute are rightly independent from the MoD and have involved external oversight and legal advice,” a spokesman said. “After careful consideration of referred cases, the independent Service Prosecuting Authority decided not to prosecute.”

Quizzed about the claims on the BBC’s Andrew Marr Show on Sunday, Foreign Secretary Dominic Raab said UK prosecuting authorities for the armed forces were “some of the most rigorous in the world”.