A total of 87 passengers were on the NorthLink Ferries vessel MV Hjaltland when it was decided to wait for better conditions before trying to disembark at lunchtime.
A spokesman for the company said there were "atrocious wind and wave conditions" that prevented safe entry into Aberdeen Harbour.
They said a change of wind direction meant that a southbound run to Rosyth on the Firth of Forth would offer a "more comfortable" journey for passengers.
A spokesman said: "We looked at Rosyth as an alternative earlier today but discounted it because the severe south-westerly winds would have made for an extremely uncomfortable journey.
"The wind is now blowing more from an easterly direction and that will allow us to make the trip south a little easier.
"The strong winds and wave conditions around Aberdeen were showing no signs of abating.
"Our staff are now making arrangements for the passengers to be met at Rosyth and to provide them with onward transport to Edinburgh or back up to Aberdeen."