An apparent prank could have had disastrous consequences in the Hokianga after a navigation marker was repainted, Northland Harbourmaster Jim Lyle says.

The East Cardinal Mark, a riveted cast iron structure on Takataka Rock at the northern end of the Hokianga Harbour's Narrows, did have a black top and bottom section with a yellow middle - an internationally recognised colour system to assist with safe navigation.

Over the past few weeks someone had repainted it white with a blue stripe. The motivation for the prank was unclear, although Mr Lyle had been advised the look "happens to be the colour of the local rugby team".

He said the repaint was discovered and reported by the local Coastguard during a training trip and while the apparent prank might seem amusing to some, he was unimpressed.

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"There are a number of issues associated with the illegal painting of the structure, the most important being the risk to safety of mariners," he said.

It's an offence under the council's bylaws and the Maritime Transport Act to damage or deface an aid to navigation, with a fine up to $10,000. The council has issued a navigation warning and now faces costs of 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."

Mr Lyle said removing the paint will depend on favourable weather, require scaffolding and the marker can only be accessed from the water.

Equipment will need to be ferried to the rock, which requires suitable vessels, and all the work is unscheduled and comes just before the maritime team's busy summer season starts.

The matter has been reported to police and if an offender is located, the council will try to recover some of the extensive costs.