Police insist they have not been duped by the intelligence services after an investigation starkly contradicted a coroner and found that a spy found dead in a locked holdall probably died alone in an accident.
Deputy Assistant Commissioner Martin Hewitt said it was "beyond credibility" that he had "the wool pulled over my eyes" by MI6 and GCHQ, despite his team reaching entirely different conclusions to coroner Dr Fiona Wilcox, who said last year that it was likely the codebreaker was unlawfully killed.
Mr Williams, 31, was found dead in the locked bag in the bath at his flat in Pimlico, central London, on August 23, 2010.
None of his DNA was found on the padlock on the bag and there were no palmprints on the rim of the bath. The heating had been left on in the flat, despite it being summer, and MI6 failed to raise the alarm about his disappearance for more than a week.
Mr Hewitt said: "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.
"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."
However he admitted: "No evidence has been identified to establish the full circumstances of Gareth's death beyond all reasonable doubt."
Mr Williams's family still believe that he was unlawfully killed, and released a statement to say that they were "naturally disappointed" about the lack of conclusions in the case.
They said: "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. "
In May last year at the end of the inquest, Dr 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, and that "the cause of his death was unnatural and likely to have been criminally mediated".
Pathologists said he would have suffocated within three minutes if he was alive when he got inside the 32-inch by 19-inch holdall.
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, they looked for a second time at the code-breaker'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 said that officers had been given full access to details of Mr Williams' s employment.
"It is highly unusual for us to be able to go into those organisations and to have open access to personnel files, to vetting files and to all the other aspects of Gareth's work, which we have been given, and which allows us to draw the conclusion that I am convinced that Gareth's death was in no way related to his work either current or previously."
Initially, a team of counter-terrorism police officers had acted as a go-between for the murder squad and the security services, but this was changed in the wake of the inquest.
Mr Hewitt said: "We didn't get it right at the beginning and the way that we did it was cumbersome and didn't allow us to do the investigation in the way that we wanted to.
"We recognised that fact and we changed it fundamentally for the subsequent two years of the investigation. I don't think that process stopped us getting any evidence that we needed to get."
There are 10 to 15 unidentified DNA samples that were recovered from the flat but police said there is no positive evidence of a third party being present when Mr Williams died, or anything to suggest a "forensic clean" of his home.
"There is no evidence whatsoever to support the suggestion that Gareth's flat had been subject to some form of 'forensic clean'," Mr Hewitt said. "Indeed, fingermarks and traces of DNA going back some years have been recovered, which tends to fundamentally disprove such a theory. Such a 'selective' clean would not be possible."
Mr Williams had looked at bondage websites but nothing specific about getting into bags.
His family expressed anger that MI6 took so long to check what had happened to him.
They said: "We still, however, remain very disappointed over the failure of his employers at MI6 to take even the most basic inquiries concerning Gareth's welfare when he failed to attend for work on August 16 2010.
"We believe that if proper steps had been taken in the same manner as any reasonable employer would have undertaken, further information relating to the cause of his death might have become apparent and not have been lost due to the length of time before Gareth's body was found.
"This lack of concern for Gareth's wellbeing remains an overriding feature of our thoughts following the death of a dear son and brother."
No request has been made to the Attorney General's office for him to apply to the High Court to have the inquest verdict quashed.