Scotland Yard today put itself at odds with the findings of a coroner and the family of MI6 codebreaker Gareth Williams by announcing that he had most probably died by accident when his body was found in a locked bag.

An inquest last year found that Mr Williams, whose remains were discovered inside a sports holdall in a bath with no evidence of his DNA on the padlock used to close it, had "on the balance of probabilities" been killed unlawfully in August 2010 while he was working for the Secret Intelligence Service while on secondment from GCHQ.

The finding by Westminster coroner Dr Fiona Wilcox prompted a reinvestigation by the Metropolitan Police lasting a further 12 months which officers said had been allowed unprecedented access to serving MI6 staff following strong criticism at the inquest of the spying agency's actions following the death of Mr Williams.

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But a senior Yard officer announced that despite a re-examination of all evidence and the investigation of new leads no definitive answers had been obtained as to the cause of Mr Williams' death and the "most probable scenario" was that he had died alone in his flat in Pimlico, central London, as the result of accidentally locking himself inside the bag.

Deputy Assistant Commissioner Martin Hewitt told a press briefing at New Scotland Yard that while there was no evidence to conclusively explain the death of the 31-year-old codes expert, police were now able to draw a different "logical inference" from that of Dr Wilcox, who had found that the death was "likely to have been criminally meditated".

Mr Hewitt said: "With the conclusion of the investigation, the MPS 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… there exist evidential contradictions and gaps in our understanding."

The Yard said Dr Wilcox had accepted the findings of the investigation but had decided there was insufficient evidence for her to apply to re-open her inquest and consider fresh findings.

But the family of Mr Williams, a maths prodigy from Anglesey, said they believed that the conclusion of Dr Wilcox that foul play was the most likely cause of the GCHQ specialist's death - and that the involvement of the security services could not be ruled out although there was no evidence to that effect - remained valid. Among the lines of inquiry reportedly pursued by police was the theory that Mr Williams may have been murdered in connection with work that had brought him into contact with active MI6 agents.

In a statement, the family said: "We consider that on the basis of the facts at present known the coroner's verdict accurately reflects the circumstances of Gareth's death."

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The family were also sharply critical of MI6 after the spying agency failed to investigate his failure to attend work on 16 August 2010. His decomposing remains were not found until a week later inside his MI6-owned flat, where the central heating had been left on despite the summer weather.

The statement said: "We believe that if proper steps had been taken in the same manner as any reasonable employer would have taken, 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."

The Yard said that it had studied videos which emerged following last year's inquest showing how a person could lock themselves inside a sports bag and accepted it is "now proven" that such an event could have happened with the same North Face holdall and padlock in which Mr Williams was found.

Mr Hewitt said he believed that evidence pointed out by Dr Wilcox as significant, such as the absence of any palm prints from Mr Williams on the bath, could be explained by him not having touched it as he got into the bag but he accepted other evidence, such as the absence of the victim's DNA on the padlock, remained unexplained. He added that there was no evidence that Mr Williams' interest in bondage or escapology was linked to his death.

Mr Hewitt said his officers had been allowed to interview 27 MI6 and GCHQ employees after it emerged during the inquest that direct access had not been given to investigators following Mr Williams' death and potential evidence, including memory sticks and a bag found under his desk, had not been made available.

The officer admitted that the Yard "did not get it right" in its arrangements with MI6 but said it had now received full co-operation. He rejected suggestions that the intelligence agency had been able to "pull the wool over my eyes".

The Yard said it was no longer pursuing any active lines of enquiry but the case would remain review. The re-investigation found 10 to 15 traces of DNA which current technology is unable to develop into full profiles. All other DNA and fingerprints in the flat had been eliminated.