Deputy Assistant Commissioner Martin Hewitt said MI6 worker Gareth Williams' 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 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."