The UK’s chief of defence staff has said the inquiry into alleged murders by special forces personnel in Afghanistan will be an “emotive and uncomfortable process for some”.

Admiral Sir Tony Radakin told the chairman of the inquiry that the probe should “not take away from the effort and commitment of the many thousands” of soldiers from the UK who served in the war-torn nation.

The defence chief said it is “right that allegations of unlawful activity are thoroughly investigated”, and said the Ministry of Defence’s (MoD) involvement is about “justifying our reputation”.

The inquiry will examine whether special forces had a policy of executing males of “fighting age” who posed no threat in Afghanistan between 2010 and 2013.

Afghan families have accused UK special forces of conducting a “campaign of murder” against civilians, while senior officers and personnel at the MoD “sought to prevent adequate investigation”.

Concluding his evidence to the inquiry on Tuesday, Admiral Sir Tony said: “I’d like to take this opportunity to reiterate the Ministry of Defence’s support for this inquiry.

“We recognise this inquiry is focused on the conduct of deliberate detention operations within a very specific three-year period and the subsequent response by the Ministry of Defence.

“It should not take away from the effort and commitment of the many thousands of British personnel who were deployed to Afghanistan over a period of more than two decades, and who … risked their lives, and many of whom lost their lives and also suffered injuries.”

The defence chief continued: “We’re also very clear that this involves justifying our reputation, and to maintain public confidence now and for the future – and it’s right that allegations of unlawful activity are thoroughly investigated, and it’s right that we look at the MoD’s response to consider whether further lessons need to be learned.

“That is why the Government established this independent inquiry and it’s why the inquiry has the full support of both me and the permanent secretary and also the full support of the service chiefs.

“We acknowledge that this will be an emotive and uncomfortable process for some, but the MoD is committed to supporting our people throughout this undertaking.

“I’d like to take this opportunity to thank our servicemen and women for their understanding and their co-operation, and I’m grateful to them for their support to this inquiry.”

The probe will look at allegations that “numerous” killings were carried out, as well as the alleged cover-up of illegal activity and inadequate investigations by the Royal Military Police (RMP).

Two RMP investigations, codenamed Operation Northmoor and Operation Cestro, will be scrutinised by the inquiry.

No charges were brought under Operation Northmoor – a £10 million investigation which was set up in 2014 to examine allegations of executions by special forces, including those of children.

Operation Cestro saw three soldiers referred to the Service Prosecuting Authority, but none of them was prosecuted.

The inquiry will now hear submissions on behalf of the families of 33 people, including eight children, who were allegedly killed by special forces.

The inquiry continues.