Water is being pumped off the Royal Yacht Britannia after it started listing while being moved to have its hull repainted.
The yacht, which is now a tourist attraction in Edinburgh, is listing on the starboard side.
The fire service has been pumping water from the yacht.
It was due to be moved earlier on Friday 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.
In July, the Queen's grand-daughter Zara Phillips and England rugby star Mike Tindall hosted a pre-wedding party on board the vessel.
Spokesman Bob Downie, chief executive of the Royal Yacht Britannia, said: "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.
A major part is painting the area of the hull which is below the waterline.
Britannia has to be taken out of the water and into the dry dock to allow that part of the hull to be inspected, treated and then repainted.
Britannia served the Queen for 44 years, carrying her and the royal family on 968 official voyages.
Launched in April 1953 at John Brown's Clydebank Shipyard, Britannia was commissioned for service the following January.
It travelled 1,087,623 nautical miles, calling at more than 600 ports in 135 countries.
It was taken out of service in 1997.