The death of Gareth Williams, the MI6 officer who was found naked in a padlocked holdall in the bath at his London flat, was "criminally mediated", a coroner has said.

On the balance of probability, Williams was "unlawfully killed", Fiona Wilcox concluded, although she had earlier said there was not enough evidence to deliver a formal unlawful killing verdict.

Wilcox's finding was delivered at the end of a narrative verdict that took her two hours to deliver and in which she criticised the behaviour of MI6 and SO15, the Metropolitan police counter-terrorism unit, whose officer operated as a conduit between the intelligence service and detectives investigating Williams's death.

The head of the intelligence service made an unreserved apology to Williams's family over the delay in reporting him missing and the subsequent anguish it caused.

Wilcox, the Westminster coroner, delivered the finding after starting her verdict by saying that it was unlikely Williams's death would ever be satisfactorily explained.

Most of the fundamental questions of how he died remained unanswered, Wilcox said on the eighth day of the inquest.

After the verdict Williams's family, in a statement read out by their solicitor Robyn Williams, said their grief at Gareth's death had "been exacerbated by the failure of his employers to make even the most basic inquiries into his whereabouts and welfare".

The statement continued: "We are extremely disappointed at the reluctance and failure of MI6 to make available relevant information."

The family would be asking the Metropolitan police commissioner, Bernard Hogan-Howe, to review how the investigation into Williams's death should proceed given the "inadequacy" of SO15's investigation as highlighted at the inquest.

DCI Jackie Sebire, from the Met's homicide and serious crime command, said officers were now following the many new lines of inquiry which had emerged during the inquest. Refusing to take questions about the criticism levelled at the role of the counter terrorist officers assigned to liaise with MI6, Sebire said: "We have heard seven days' worth of evidence of the life and death of Gareth this week. I have always been satisfied that a third party may have been involved in his death and the coroner has confirmed that."

The investigation would refocus and actively pursue all the evidence heard and all the new lines of inquiry. William's body was found "in the most suspicious circumstances", Sabire said.

"It is highly likely that a third party was involved and I urge anyone who knows Gareth who had contact with him to search their consciences and come foward with any information about what happened that night, 16 August 2010.

"We would also ask anyone with any information to please come forward … to give Gareth's family some peace and allow them to grieve and move on."

During her verdict, Wilcox rejected "suicidal intent", interest in bondage or cross-dressing, or "auto-erotic activity" being related to Williams's death.

Williams, 31, a codes and ciphers expert, was about to return to GCHQ in Cheltenham after secondment to MI6 in the capital when his body was found in the flat in Pimlico in August 2010.

It emerged on Tuesday, towards the end of seven days of evidence from 39 witnesses, that memory sticks found among his possessions were examined by the Secret Intelligence Service but never handed over to detectives investigating his murder.

Wilcox said it remained a "legitimate line of inquiry" that the secret services were involved in Williams's death as she criticised "shortfalls" in MI6 passing on evidence to Scotland Yard. But there was no evidence that he died at the hands of spies.

"It would appear that many agencies fell short" during the investigation, Wilcox said, identifying breakdowns in communication by her own office in ordering a second postmortem, a DNA mix-up by forensics and the late submission of evidence by MI6 to police.

But the coroner added that "taking all these shortfalls together, I am satisfied that the evidence is reliable and that we do not have to adjourn at this point".

Wilcox said the "highly unusual circumstances" of Williams's death had immediately raised the possibility of foul play, which had prompted "endless speculation".

Williams's colleagues were interviewed but no formal statements were taken, she noted.

"I find that this did affect the quality of the evidence that was heard before this court," she said. Wilcox had almost adjourned the inquest due to late evidence, the fault of the SO15 counter-terrorism officer who was the conduit between MI6 and the police. The officer should have passed on an inventory of items found at Williams's MI6 office, said Wilcox.

Evidence from the office was important because Williams "didn't socialise much" and was a reason DNA had been taken from some work colleagues.

Wilcox said she found it "highly unlikely" that Williams got inside the bag alone, saying a lack of hand and footprints in the bathroom was significant. "In relation to the prints found within the bathroom, in my view what was more significant was what was not found rather than what was found."

A lot of time and resources had been spent during the investigation looking into a swab taken from Williams's left hand that appeared to indicate third-party involvement.

But the sample "unfortunately" was later found to belong to a forensic scientist working on the case, she said. "If Gareth had been carrying out some kind of peculiar experiment, he wouldn't care if he left any foot or fingerprints."

Wilcox appeared to rule out that Williams died as a result of some kind of "auto-erotic activity", also denying there was any evidence to suggest claustrophilia – the love of enclosed spaces – was of any interest to him.

She also dismissed the idea that an interest in bondage had any link to his death. If it had, she would have expected "much more internet activity" on the web. Williams had only visited sites on four days, she said. He was a "scrupulous risk assessor" and would have had a knife to escape.

Rejecting speculation that he was a "transvestite" spy, Wilcox said leaks that William was a "cross-dresser" could have been an attempt "by some third party to manipulate a section of the evidence".

Makeup found in his flat was more likely to reflect his interest in fashion, she argued. Wigs found there were "far more consistent with dress-up such as attendance at a manga conference", she added.

Williams's interest in female footwear could have been of a sexual nature, but this was not unusual. "Gareth was naked in a bag when he was found, not cross-dressed, not in high-heeled shoes," she said.

Williams's body was not discovered until a week after he died. Wilcox said his line manager had done "nothing effective" to establish his whereabouts when he was missing. She said she could only speculate as to what effect not reporting him missing sooner had had on the investigation.

Despite '"lots of speculation", there was no evidence Williams's death was linked to his work, she said.

His death was of "unnatural cause", she said. It was possible, but unlikely, that Williams had died in the bag when it was outside the bathroom, but she believed he was alive when he entered the bag and accepted the pathologist's evidence that suffocation or poisoning was the probable cause of death.

She was satisfied "so I am sure" that a third party had moved the bag containing Williams into the bath. There were two possible explanations: that Williams entered the bag outside his bathroom, and the bag was carried in there by a third party, or that he was locked in the bag by a third party and that was lifted into the bath.

Wilcox had earlier ruled out a formal "unlawful killing" verdict because the evidence available was not of the criminal standard needed for such a verdict. She also said an open verdict would not do justice to the "positive findings" she could make.

John Sawers, chief of the Secret Intelligence Service, expressed the "deepest condolences" of MI6 and GCHQ for the death.

In a statement delivered by MI6 lawyer Andrew O'Connor, Sawers said the service should have acted more swiftly when Mr Williams failed to turn up to work in August 2010.

He said: "On behalf of the whole organisation, Sawers regrets this deeply and apologises unreservedly."

The MI6 chief added: "lessons have been learned, in particular the responsibility of all staff to report unaccounted staff absences".