The bizarre case of a British spy who was found dead in a padlocked bag looks set to remain a mystery, after police said that a lack of conclusive evidence proving third-party involvement led them to believe he had “probably” died alone.

Scotland Yard officers – who have been investigating the case for three years – said they did not think GCHQ codebreaker Gareth Williams had been killed by the security services or any other organisation or individual.

This directly contradicts a coroner’s finding last year that the death of 31-year-old Williams was “unnatural and likely to have been criminally mediated”.

Presenting his conclusions Martin Hewitt, deputy assistant commissioner of the Metropolitan Police, said he could not categorically rule out anyone else being involved, but that the most likely explanation was that the death had been an accident.

“The most probable scenario is that Gareth was alone,” Mr Hewitt said. “Our investigation concludes, therefore, that despite extensive enquiries . . . no evidence has been identified to establish the full circumstances of Gareth’s death beyond all reasonable doubt.”

He added that there were “evidential contradictions and gaps in our understanding” that prevented investigators reaching a firm conclusion.

These findings have been accepted by the coroner, who has decided against taking the unusual step of reopening the inquest. But the dead man’s family share the coroner’s original suspicion that an undetected third party must have been present at the time of his death.

The codebreaker was found in August 2010 locked inside a 32-inch by 19-inch holdall, made by the North Face brand, which was placed in the bath of his London flat. Pathologists at the inquest said he would have suffocated within three minutes if he was alive when he got inside the bag.

Police acknowledge that some evidence – such as the lack of Williams’ DNA on the padlock, and the fact that his palm prints were not found on the rim of the bath – does suggest that he did not get into the bag himself.

However, Mr Hewitt said that there was nothing to suggest that he had been involved in a struggle, or that the flat had been broken into. The detective also disputed theories that the Pimlico flat had been “deep cleaned’’ to remove forensic material before police arrived, given that plenty of background DNA was found in the flat, some dating back several years.

Williams was seconded to MI6 at the time of his death, and the agency initially resisted police efforts to question their staff about the incident. After the inquest, police detectives were finally given access to the codebreaker’s personnel and vetting files, and interviewed 27 secret intelligence service and GCHQ staff about their colleague.

When asked whether it was possible that the secret services had managed to conceal or cover up some clues about Williams’ death, Mr Hewitt was adamant this had not been the case.

“I do not believe that I have had the wool pulled over my eyes,” the detective said. “I believe that what we are dealing with is a tragic unexplained death.’’

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