Vice Admiral Clive Johnstone said the spread of the organisation in Libya had cast an “uncomfortable shadow” over the sea.
Johnstone said that Isis was keen to build a navy to carry out attacks.
“We know they have had ambitions to go off shore, we know they would like to have a maritime arm, just as al Qaeda had a maritime arm,” he said.
He added: “There is a horrible opportunity in the future that a misdirected, untargeted round of a very high quality weapons system will just happen to target a cruise liner, or an oil platform, or a container ship.”
Johnstone was speaking onboard a Spanish Nato ship in London.
He said an attack on a ship would likely be a mistake or a random act of terrorism and that while there is no current threat, Nato had watched Isis “grow and morph in such extraordinary ways”.
*Update*
Cruise body Clia UK and Ireland said in a statement: "As always, cruise lines coordinate closely with national and international security and law enforcement authorities around the globe to help ensure passenger safety.
"While we cannot disclose specifics of cruise ship security protocols, cruise lines take passenger safety very seriously. Security staff are well-trained and experienced; some are former law enforcement officers. Port and onshore facilities, infrastructure, and passenger security and services in destinations are strictly scrutinized.
"In the event of any safety concerns, cruise ships have the flexibility to alter their itineraries as needed to avoid areas of higher risk. Our priority is to provide for the safety of passengers and crew at all times."
