Cyclone brings fresh flood threat to sodden towns

It was still packing wind gusts of up to 130km/h with the capacity to cause damage to some homes having gathered strength while over the Gulf of Carpentaria overnight.

The Bureau of Meteorology said the cyclone was the first weather system in more than two decades that was expected to hit three states and territories.

Cyclone Narelle crossed Cape York in far-north Queensland on Friday as a category-four system - the second-highest classification.

It is expected to weaken to a tropical low as it tracks across the Northern Territory towards Katherine, a major town that has already been struck by widespread flooding from a previous storm.

Shelter warnings are still in place from Nhulunbuy to Numbulwar in Arnhem Land.

Narelle is expected to move over the Joseph Bonaparte Gulf on Monday and gales are forecast to develop to the north of the centre.

There is a moderate chance that Narelle redevelops into a tropical cyclone while in the gulf and near the border with Western Australia.

"Do not venture outside if you find yourself in the eye of the cyclone," the bureau warned in a morning update.

"Very destructive winds from a different direction could resume at any time."

Towns on the Gulf of Carpentaria and further inland in the Northern Territory have been told to expect wind gusts up to 165km/h and rainfall above 200 millimetres on Sunday.

The community was well-prepared for the storm and the government response so far had been effective, the director of the Savannah Way Motel in the gulf town of Borroloola said.

"There has been a fair bit of water around from previous rain," Anastasi Kambourakis told AAP.

"Most of the people who live in Borroloola are used to it this time of year."

Narelle is the first cyclone to hit the area in more than a year and lessons have been learned from previous experiences.

"We did lose freight for a little bit," Mr Kambourakis said.

"The government always prioritises getting it through to the community."

Gulf communities are also warned to expect abnormally high sea levels that could cause flooding of low-lying areas.

Residents sheltering at home should move to the smallest, strongest, most protective room in their house, such as a bathroom or a toilet.

Flood warnings are in place across much of the Top End, particularly in Katherine and the previously inundated community of Daly.

Patients were evacuated from Katherine Hospital in anticipation of Narelle worsening the delicate flood situation in the town.

Warnings are also in place for large swathes of WA.

People across the Kimberley have been told to prepare now for the likelihood of heavy rain on Monday as the storm slowly weakens.

In Queensland, the clean-up from the cyclone has begun with energy crews deployed to return to power more than a 1000 homes.

Police have delivered fuel to remote communities on Cape York to help locals recover from the storm, which brought down trees and ripped off roofs as it passed.