Staff at the Roman Palace and Gardens at Fishbourne called in engineers after they noticed that part of the mosaic had become waterlogged.
A corroded pipe was found and the museum activated its disaster plan.
In August 1960 workers trying to lay the same pipe uncovered the ruins at Fishbourne near Chichester.
They found a Roman boundary wall and the remains of the palace with 20 floor mosaics followed.
Richard Keates, of Portsmouth Water, said: "The company has always been rather proud of the part its predecessors played in the discovery of the palace although more recently we have recognised that a major supply main lies in very close proximity to such important artefacts.
"We were very pleased with the level of co-operation that we received from the staff and volunteers at Fishbourne which enabled us to complete the repairs very quickly."
Portsmouth Water said it wanted to move the pipe away from the artefacts in the new year.
Museum director Christine Medlock said: "We are hoping that our swift action and the work of Portsmouth Water will mean that damage to the mosaics will have been kept to a minimum.
"We were able to remain open with little disruption for visitors."
A 2,000-year-old Roman mosaic has been been protected from a water leak from a pipe that led to its discovery in 50 years ago.