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Deputy Assistant Commissioner Martin Hewitt, of the Metropolitan Police, says there remains "gaps in understanding" regarding the death of MI6 worker Gareth Williams.
But he has concluded, following two years of investigation, that it is "most probable" that the codebreaker was alone at the time of his death.
The family of Gareth Williams, who was found dead in a holdall, have said the unknown circumstances of his death "adds to their grief".
Police said it had concluded that spy Gareth Williams probably died alone in an accident, but admitted there was no evidence to establish the circumstances of his death "beyond all reasonable doubt".
The family statement read: "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. "
The family said they remain disappointed that Gareth William's employers at MI6 failed to make inquiries into his welfare when he failed to attend work in the days before his body was found.
The family of Gareth Williams's family said they were "naturally disappointed" by the conclusions of the Met Police, and said they still believe he was killed.
Gareth Williams was found in a bag in the bath at his flat in Pimlico in 2010. Pathologists said he would have suffocated within three minutes if he was alive when he got inside the 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.
Spy Gareth Williams, whose body was found in a holdall in Pimlico, probably died alone in an accident. Met Police said today they disagree with the conclusion of a coroner last year that the codebreaker was probably killed unlawfully.
Deputy Assistant Commissioner Martin Hewitt 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."