Police deployed aircraft with heat-seeking equipment in the search
The shattered remains of John Darwin's red kayak were found washed up on a beach in Seaton Carew, near Hartlepool, in March 2002.
An extensive search was launched but no trace was ever found of Mr Darwin, who was then aged 51.
"It is not known at this time where he has spent the last five-and-a-half years," said a police spokesman.
Cleveland Police said that Mr Darwin, a married father-of-two, walked into the West End Central Police Station in London at 17.30 GMT last night.
The spokesman added: "Mr Darwin is fit and well and relatives have been informed of his whereabouts."
Mr Darwin's disappearance sparked agony for his family.
John Darwin, 51, was seen entering the sea in the Seaton Carew area with his kayak at 0800 GMT on Thursday 21 March 2002.
At the time Mr Darwin was working as a prison officer, and the alarm was not raised until 21.30 when it was reported he had failed to arrive for a night shift.
Police and coastguard officers searched the coastline from Hartlepool down to Staithes, North Yorkshire, deploying five RNLI lifeboats, two coastguard rescue teams and a police fixed-wing aircraft with heat-seeking equipment - to no avail.
His wife Anne, a doctor's receptionist, said six months after her husband vanished: "People die, have a funeral, they have a headstone, there is something to mark the fact they existed on this earth.
"But without a body, I don't know how we can mark John's life.
"All I want is to bury his body. It would enable me to move on. It's difficult to grieve without bringing things to a close, but as it is I'm in limbo and there's nothing I can do."