Craig Townsley, 22, from Shetland, was last seen on the Shetland to Aberdeen overnight ferry at around 3.30am on Monday.
His disappearance from NorthLink's MV Hjaltland prompted a major search off the north-east coast of Scotland.
The operation, co-ordinated by the Maritime and Coastguard Agency, was eventually stood down at 8pm on Monday after failing to trace Mr Townsley. At its height, it had involved a number of commercial vessels, three RNLI lifeboat teams and two helicopters.
Police said the case remains a missing person inquiry and Mr Townsley's family have been made aware of developments.
Detective Inspector Stewart Mackie said: "Our initial inquiries indicate that Mr Townsley may have gone overboard."
The RAF helicopter Rescue 137, from Lossiemouth, and the Coastguard helicopter Rescue 102, from Shetland, joined the search, along with RNLI crews from Fraserburgh, Peterhead and Aberdeen, as well as 22 merchant boats.
The ferry was close to Aberdeen when it raised the alarm. It retraced its route to help with the search but later docked at Aberdeen.
The search focused on a long, thin stretch of water on the ferry route from just north of Aberdeen up to Rattray Head.