Spy Gareth Williams, whose body was found in a holdall, probably died alone in an accident, police have concluded.
Deputy Assistant Commissioner Martin Hewitt revealed that his team disagree with the conclusion of a coroner last year that the codebreaker was probably killed unlawfully.
He said: “With the conclusion of the investigation, the Metropolitan Police’s position is that, on balance, it is a more probable conclusion that there was no other person present when Gareth died.
“But the reality is that for both hypotheses there exist evidential contradictions and gaps in our understanding.”
Reacting to the development, Mr Williams’s family said they were “naturally disappointed” and said they still believe he was killed.
But Mr Hewitt said the 31-year-old’s death was “most probably” an accident, although he admitted: “No evidence has been identified to establish the full circumstances of Gareth’s death beyond all reasonable doubt.”
Mr Williams, a fitness enthusiast originally from Anglesey, was found in the bag in the bath at his flat in Pimlico, central London, on August 23, 2010.
Pathologists said he would have suffocated within three minutes if he was alive when he got inside the 32-inch by 19-inch holdall.
None of his DNA was found on the lock on the bag and his palm prints were not found on the rim of the bath.
However, Mr Hewitt said there was no evidence that the flat had been “deep-cleaned” to remove forensic traces and nothing to suggest a struggle or a break-in.
He said it was “beyond credibility” that the secret services had “pulled the wool” over his eyes.
“I do not believe that I have had the wool pulled over my eyes. I believe that what we are dealing with is a tragic unexplained death.”
Mr Williams’s family said in a statement issued through the police: “We are naturally disappointed that it is still not possible to state with certainty how Gareth died and the fact that the circumstances of his death are still unknown adds to our grief.
“We consider that on the basis of the facts known at present the Coroner’s verdict accurately reflects the circumstances of Gareth’s death. ”
Mr Williams worked for GCHQ but was on secondment to MI6 when he died. Police interviewed a total of 27 members of staff from the two agencies as part of their investigation.
Following the inquest, which finished in May last year, they were also given access for the first time to the codebreaker’s personnel and vetting files, but found that there was “no evidence to support the theory that Gareth’s death was in any way related to his work”.
Mr Hewitt went on: “Three years of extensive investigative activity have developed a very clear profile of Gareth. He was, without doubt, a private person who was very close to his family and had few other close friends. That said, the universal view of colleagues was of a conscientious and decent man with a few well-known hobbies such as his cycling and climbing.
“There is no evidence of any animosity towards Gareth, and it has not been possible to identify anyone with a motive for causing him harm.”
Last year coroner Dr Fiona Wilcox found that he was probably killed and it “remained a legitimate line of inquiry” that the secret services may have been involved in the death.
She said she was sure a third party locked the code-breaker inside the red holdall in which his naked body was found in his bathtub.
Mr Williams would have been unlikely to invite a third party who was not a family member into his home, Dr Wilcox observed, adding: ”If a third party was present at the time of his death, in my view that third party would have to have been someone he knew or someone who was there without an invitation.”
She warned it was unlikely the mystery would ”ever be satisfactorily explained”, but added: “The cause of his death was unnatural and likely to have been criminally mediated.
“I am therefore satisfied that on the balance of probabilities that Gareth was killed unlawfully.”
She highlighted the lack of hand and footprints found in the bathroom, and said if he had been ”carrying out some kind of peculiar experiment, he wouldn’t care if he left any foot or fingerprints”.
Police said that Dr Wilcox has accepted their findings, but decided that there is insufficient new evidence to justify re-opening the inquest.