Lyle said the motivation for the prank was unclear, although he had been advised the beacon's new unauthorised scheme "happens to be the colour of the local rugby team".
He said the repaint was noticed and reported by the Coastguard during a training trip. The stunt might seem funny to some but his office took a very dim view of it, Lyle said.
"The matter had been reported to police, who have been asked to assist in finding whoever was responsible.
"There are a number of issues associated with the illegal painting of the structure, the most important being the risk to safety of mariners."
Lyle said it was an offence under the council's bylaws and the Maritime Transport Act to damage or deface an aid to navigation and those responsible could be fined up to $10,000.
The council has issued a formal navigation warning through the local Coastguard radio station to warn harbour users about the incorrectly coloured beacon and faced "significant" costs of many thousands of dollars to repaint it.
"Unfortunately we can't just slap more paint over the top of an unknown paint," he said.
"Painting structures exposed to salt environments requires correct preparation, and high quality paint systems."
Lyle said removing the paint was also quite difficult as it would depend to some extent on favourable weather. Scaffolding would also be needed as the marker could only be accessed from the water.
Equipment would have to be ferried to the rock on suitable vessels - just before the maritime team's busy summer season starts.
Lyle said the council would try to recover some of the extensive costs from any offender who could be identified.
Meanwhile, he said the council will take advantage of the forced repaint to do unrelated engineering work on the structure.
