And local authorities suggest that and their heritage significance is the only thing they should be famous for.

Not the vandalism that occurred in a graffiti attack on Thursday night.

The large lighthouse at Flagstaff Hill and the smaller Breakwater Lighthouse to the entrance to Wollongong Harbour were targeted just hours before rallies were held in Wollongong and 100 other locations around the nation calling for climate justice.

Early morning joggers, walkers and cyclists made the discovery just after dawn on Friday.

They saw the words Climate Justice Now written prominently in red paint on both lighthouses.

Wollongong Lord Mayor Gordon Bradbery said there were better ways to get the message across than defacing such iconic structures in the city.

"I can understand people's passions and concerns about climate change and the issues that confront us but to put graffiti on the lighthouse was not exactly a smart move," he said.

"It might have brought attention to their cause but at the same time it has brought a negative response.

"I fully appreciate the passion of the people involved but at the same time council and the community are worried about graffiti of that nature especially on an asset like that".

Cr Bradbery said council crews were quick to clean much of the red paint off the two lighthouses on Friday morning.

On Monday council will paint over what is left with white paint.

Benjamin Gava found the graffiti on his early morning jog just before 6am and was sympathetic to the cause.

"I was quite surprised to see it at first, but the more I thought about it the more I felt "good on them, whoever it was". I think most people understand that we are facing a climate emergency and that more needs to be done to limit climate change and its detrimental impacts," he said.

Other onlookers were not so sympathetic and horrified that anyone would do that to two such important landmarks.

Lighthouses of Australia president Ian Clifford is he is aware of the cause and what was trying to be highlight on Friday. But he was surprised that anyone who genuinely believes in such a cause would go to such lengths.

"It is not a great way to highlight the cause," he said.

Mr Clifford informed the organisations responsible for looking after the two lighthouses to inform them of the mess made overnight. He said NSW Police were also being informed.

Mr Clifford said graffiti on the two lighthouses was fairly rare.

"Nationally we don't have much of a graffiti issue with the lighthouses. From time to time we get a little bit of it in Wollongong. It often occurs on a Thursday night".

Mr Clifford said Lighthouses of Australia activate the Breakwater Lighthouse, which is not an active lighthouse, once a year to demonstrate its operation.

That occurs on the mid weekend in August. It is turned on for four nights from Thursday to Sunday.