The defence secretary has said that he has “confidence” in his senior officers and their ability to lead after they were embroiled in a war crimes scandal.

John Healey said that he “absolutely” believed General Sir Roly Walker, the head of the army, and General Sir Gwyn Jenkins, about to become head of the navy, had integrity.

Both generals were named in a BBC Panorama investigation on Monday night, which claimed that members of Britain’s special forces murdered innocent Afghans over more than a decade.

Lieutenant General Sir Roland Walker at a service for Admiral Lord Boyce.

General Sir Roly Walker

MAX MUMBY/INDIGO/GETTY IMAGES

Group photo of military and political figures at a US Marine Corps anniversary event.

Healey, left, with General Sir Gwyn Jenkins, second from right, and Lord Mandelson, right, at the British ambassador’s residence in Washington

CARLA RUTHERFORD/UK MOD CROWN

The documentary included claims that Jenkins oversaw the rejection of hundreds of UK resettlement applications from Afghan commandos who served alongside the Special Air Service (SAS) during the war.

The rejections were controversial because it is understood that some of those individuals may be able to provide testimony to the Afghan inquiry into allegations of killings because they were on the ground at the time.

The BBC has previously reported how Jenkins, the former vice-chief of defence staff and ex-director of special forces, was sent records of conversations in 2011 in which members of the special forces described extrajudicial killings.

Although he referred the information to his superior officer, he did not refer the evidence to military police and instead put it in a classified dossier and locked it in a safe, it has been claimed.

SAS accused of ‘barbaric’ war crimes in Iraq and Afghanistan

Johnny Mercer, the former veterans minister, has previously said that he did not believe an account given to him by Walker and others that allegations surrounding the killings had been properly investigated.

A clip of his testimony to the Afghan inquiry in which he said “something stinks” was aired on Monday night.

British and Afghan soldiers patrolling Sangin Valley, Afghanistan.

The documentary claims that Jenkins oversaw the rejection of hundreds of UK resettlement applications from Afghan commandos who served alongside the SAS during the war

MARCO DI LAURO/GETTY IMAGES

Asked about the documentary and whether he had confidence in Walker and Jenkins and their ability to lead and integrity, Healey said: “Yes, absolutely.”

He went on: “I’ve worked very closely with both.” He said that he had been working with Jenkins, who was his strategic advisor, to “strike a number of big export deals”. “I’ve worked very closely with Roly Walker as the new chief of the general staff as well,” he added.

Afghan allies ‘treated like dogs’ by British special forces troops

Jenkins was expected to be announced as first sea lord as soon as last week but the announcement never came.

Instead it emerged that Admiral Sir Ben Key, the first sea lord, was being investigated over allegations of an affair with a junior officer.

It is understood that ministers are still adamant that Jenkins will be handed the role as head of the navy amid concern that he has been tainted by the inquiry. One Ministry of Defence source said that Jenkins was “one of the good guys in this”, suggesting that he would be found to have done nothing wrong, a view shared by many others.

A senior navy source said that the navy was “in crisis” after Key was placed under investigation.

“We recognise this is a time of crisis for us. The remaining leadership are absolutely focused on steadying things and making sure we deliver,” the source said.

The explosive revelations about Key’s alleged affair come as the MoD is about to publish its long-awaited strategic defence review.