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Tropical Cyclone Narelle was again intensifying into a severe storm off Western Australia’s Kimberley coast on Wednesday with communities in the state’s world heritage-listed Shark Bay preparing for a potential direct hit on Friday night.

Narelle had made a rare trip for a cyclone system by forming in the Coral Sea off Queensland and maintaining structure all the way west to the Indian Ocean, where it was expected to build into a major category four system.

The system smashed Cape York last week, before rebuilding over the Gulf of Carpentaria and moving over the Top End where communities were still recovering from major flooding.

Rainfall from Narelle’s back end was still affecting the Northern Territory on Wednesday afternoon, with the Bureau of Meteorology warning of major flooding in Katherine and also at Daly River.

Jenny Sturrock, a senior forecaster at the BoM, said Narelle would be a severe category 3 system by Thursday morning and by Friday would probably build to category 4 as it goes south past the Ningaloo coast.

“There’s close agreement among the models on the corridor we expect Narelle to take,” she said.

Even though the cyclone appeared to be well offshore, wind gusts of more than 125km/h were still possible along the coast as the cyclone made its way south.

The bureau’s current forecast has Narelle making landfall after 8pm local time on Friday as a severe category 3 storm over the tourism town of Denham in the world heritage-listed Shark Bay.

Peter Stubberfield, a councillor and president of the Shire of Shark Bay council, said the town was “pretty apprehensive” for what could be coming.

The closest major centre to Denham, which has a population of about 700 but can swell to thousands with tourists, is more than four hours away in Geraldton.

Caravan parks were evacuating, he said, and travellers were being advised to leave the town and head south “and don’t stop at Geraldton”, he said.

Denham had no permanent medical services aside from a nursing station, with no doctors or hospital, Stubberfield said.

Shark Bay was placed on the world heritage list in 1991 for its “exceptional natural features”, including vast seagrass beds, dugongs and its colonies of stromatolites – which are some of the earliest life forms on the planet.

Narelle would be the region’s second cyclone in the last two months, after Mitchell clipped the town in early February as a weakening category 1 system.

“But this is a different beast to cyclone Mitchell,” he said. “The town is getting prepared and the emergency centre is being prepared.”

After making landfall, forecasts show Narelle could travel south-east and close to the city of Geraldton on Saturday.

Narelle will have travelled more than 5,500km by the time it approaches Perth. Earlier this week, some forecasts suggested the state capital could be in the path of the system.

But Sturrock said forecasts in the last 24 hours had moved the cyclone’s path further north and east, but she said the city could still see significant daily rainfall of roughly 50mm on Friday and Saturday and blustery conditions.

Dr Joseph Christensen, a historian at the University of Western Australia, is researching the history of cyclones and extreme weather in the state from the 19th century onwards.

He said most cyclones that had crossed the WA coast came through a “cyclone alley” between Broome and Onslow, north of the Ningaloo coast.

“The further south you go, the less common they become,” he said.

“In Perth, most people remember Cyclone Alby in 1978 and that is the last significant system to affect the city – that was almost exactly 48 years ago.”