An MI6 boss has expressed regret for failing to raise the alarm that Gareth Williams was missing.
The line manager said he wrongly assumed Mr Williams was stuck on a train when he missed a meeting seven days before his rotting remains were found.
Coroner Fiona Wilcox asked him why he took no action, saying: "There's a difference between being late and failing to turn up to a meeting at 3pm."
The secret services boss, who gave evidence behind a 10ft blue screen to protect his identity, replied: "In hindsight, knowing what I know now, should I have taken action? Absolutely.
"I was just working on the conclusion that Gareth was late on a train, stuck on transport."
MI6 colleagues assumed for several days that he might have been packing ahead of his return from secondment to GCHQ or working on coursework.
Dr Wilcox added: "I am really struggling to understand why you took no action at this point."
The spy, identified only as G, said: "I still had that gut feeling that he was away doing something that I was not made aware of."
Mr Williams had only recently returned from Las Vegas on a trip relating to his "wind-down" from duties and G said Mr Williams wanted to leave MI6 because he was getting bogged down in bureaucracy.
He had never failed to turn up for work before his disappearance in August 2010.