HMS Queen Elizabeth is an aircraft carrier that was supposed to lead the largest NATO exercise since the Cold War, but it will instead be heading back to Rosyth for repairs.
Meanwhile the HMS Prince of Wales, which was also built at the Babcock dockyard, will be taking its place off the coast of Norway.
The ship launched in 2017 and is a sister ship to HMS Queen Elizabeth, which launched in 2014.
Final checks before leaving Portsmouth for Scandinavia found an issue with Elizabeth's starboard propeller coupling.
The Prince of Wales returned to Fife for repairs last summer. It was found its starboard propeller had malfunctioned.
An MoD spokesperson said the issue on HMS Queen Elizabeth was "separate and not linked".
They added that they do not know when the ship will arrive in Fife as it is currently undergoing "initial investigations".
More than 40 vessels are due to take part in the NATO exercise.
Fleet Commander Vice Admiral Andrew Burns said: "Routine pre-sailing checks identified an issue with a coupling on HMS Queen Elizabeth's starboard propeller shaft.
"HMS Prince of Wales will take her place on NATO duties and will set sail for Exercise Steadfast Defender as soon as possible."
A Royal Navy spokesman said: "On completion of initial investigations, HMS Queen Elizabeth will sail for Rosyth in Scotland so any necessary repairs can be carried out in due course.
"The cause of the issue with HMS Queen Elizabeth is wear and tear of her starboard propeller shaft coupling."
The MoD spokesperson added: "The issue identified is with the ship's shaft couplings. The ship's propeller shafts are too big to be made from a single piece of metal, so each shaft is made from three sections, which are connected using shaft couplings, which bind the shaft sections together."
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