The cover-up of murders by British special forces in Afghanistan has reached very high into the military and the state.

Senior army figures were warned that British SAS units were planting evidence to try to justify killing dozens of innocent civilians during raids, an inquiry has heard.

The deaths stemmed from a policy to “execute Afghan males of fighting age” regardless of whether they were a threat.

One senior military officer said the justifications given were “logic-defying”. Other staff used internal emails to lament a “casual disregard for life”.

Details about the killings have now emerged at a long-awaited public inquiry that will investigate the behaviour of Britain’s “elite” military units over a three-year period. More than 80 Afghans were summarily killed between 2010 and 2013.

The government only allowed the inquiry after losing a court case brought by victims’ families.

Opening it in London last week, Lord Justice Haddon-Cave said it would examine claims that the allegations were “covered up at all levels over the last decade” and that investigations by the Royal Military Police (RMP) were not fit for purpose.

Raids, known as deliberate detention operations (DDOs), saw killings legitimised as acts of self-defence. In one February 2011 raid in Northern Helmand, the British killed nine people in their beds while asleep. The unit involved said it acted in self-defence.

The inquiry heard evidence from internal emails in which officials said the explanation of the raids was “bollocks”.

In April 2011 a commanding officer wrote to the commander of the British special forces. He outlined claims that a special forces sub-unit had killed people after they were restrained.

The commanding officer had earlier written a statement in which he laid out claims that British operatives had planted weapons on those they killed.

In October 2012 a night-time raid in central Helmand province seeking a suspected Taliban commander resulted in the deaths of three boys aged 12, 14 and 16 and a man of 18.

RMP personnel travelled to Afghanistan in February 2014 to interview officers about the deaths. But the chief of staff terminated an interview over what was said to be a breach of “agreed conditions”.

Investigators returned to arrest the chief of staff in Afghanistan the following month. But they were incorrectly told he was not there. Information from a security services computer server was “withheld from those tasked with looking into the allegations”.

He was arrested later alongside two soldiers who were being directly investigated in connection with the deaths. No charges were brought.

The public inquiry is expected to take 12 to 18 months to produce an interim report.

Secrecy conditions imposed by the inquiry mean large parts of it will be held without the public or press present.

The identities of any soldiers involved have been redacted, as well as the names of their commanding officers and many others in the British military. The military’s own accounts of a number of raids are not being made public.

In 2011 one member of the SAS wrote about the official description of the raids: “For what must be the 10th time in the last two weeks,” when an Afghan was sent back “to open the curtains (??) he re-appeared with an AK.

You couldn’t MAKE IT UP.” But the inquiry may shine a dim light on how they did exactly that, then how others covered it up.