Water is being pumped off the Royal Yacht Britannia after it started listing while being moved to have its hull repainted.
The yacht, which was based in Portsmouth until the late 1990s is now a tourist attraction in Edinburgh, is listing on the starboard side.
It is thought there may have been a leak in the door seal.
The fire service has been pumping water from the yacht.
It was due to be moved earlier today to a dry dock across the harbour in Leith.
Sources confirmed that a ‘small leak’ in the seal of an outer door had been discovered when they started to move the mooring lines.
There is not thought to be any other damage to the yacht.
In July, the Queen’s grand-daughter Zara Phillips and England rugby star Mike Tindall hosted a pre-wedding party on board the vessel which was attended by Princes William and Harry and the Duchess of Cambridge.
Spokesman Bob Downie, chief executive of the Royal Yacht Britannia, said: ‘When we were removing the mooring ropes this morning the ship moved four degrees to starboard.
‘This meant that new access watertight doors to our pontoons were below the water level.
‘There has been a leak in the seals in those doors which was accentuating the list.
‘Because we have limited shore power, we asked the fire brigade to provide us with some assistance in correcting the ship’s ballast.
‘This has caused a delay in the process. Britannia has been secure at all times and we hope to continue the move to dry dock later today or tomorrow.’
The ship, which shut on New Year’s Day for a month, is being moved to the neighbouring Imperial Dry Dock, also in the Port of Leith, for work to be carried out.
Britannia served the Queen for 44 years, carrying her and the royal family on 968 official voyages.
At the beginning of January 1997, Britannia set sail from Portsmouth to Hong Kong on its last and longest voyage.
On December 11 that year it was decommissioned at Portsmouth Naval Base in the presence of the Queen, the Duke and 12 senior members of the Royal Family.