Destructive wind gusts are hammering remote communities in the Top End, with tropical cyclone Fina strengthening as it nears major population centres.

Fina passed over the Cobourg Peninsula overnight and into the Van Diemen Gulf on Saturday, moving slowly to track just north of the Northern Territory capital, Darwin.

Earlier in the morning, the Bureau of Meteorology said the system had been upgraded to category three.

Severe Tropical Cyclone Fina, category 3, is expected to pass north of Darwin later on Saturday. Darwin to experience a rapid increase in winds later this afternoon and evening.

A cyclone warning zone was in place for Darwin, the Daly River Mouth to Cape Don, including the Tiwi Islands, Dundee Beach, Milikapiti, Pirlangimpi and Wurrumiyanga.

At 10.30am Darwin time, Fina had sustained winds near the centre of 130km/h with wind gusts of up to 185km/h. It was tracking 85km northeast of Darwin.

At the third tier of severity, cyclones can bring wind gusts of up to 224km/h and cause structural damage to properties.

"Very destructive wind gusts are likely about exposed coastal sites northeast of Darwin today, but the risk at Darwin is assessed as low," the weather bureau said.

The city could still cop destructive and damaging wind gusts.

Heavy rainfall could lead to flash flooding in coastal areas between the Tiwi Islands and Warruwi, extending across the western Top End including Darwin on Saturday and Sunday.

Speaking in South Africa, Prime Minister Anthony Albanese urged people in the cyclone's path to look after themselves and others.

"My thoughts are with people at this time and also with the emergency service workers and others who will be working hard," he said.

The NT Emergency Service is confident most buildings in Darwin can withstand the storm and advises people to stay at home while the destructive winds pass.

Senior meteorologist Dean Narramore said 150 to 180km/h category three winds would be near the centre of the cyclone, with winds of up to 120km/h in Darwin.

Those wind strengths would be "easily enough to cause property damage and bring down trees and powerlines", he told ABC News.

Some island locations have copped 200mm of rain in 24 hours and similar falls were expected in the Darwin area.

Mr Narramore said the impacts were highly dependent on the exact track and intensity of Fina.

"If it moves a bit further north, less impacts for Darwin, more impacts for the Tiwi," he said.

"But if it wobbles a little bit further south this afternoon, we could see more impacts in Darwin."

Alice Williams, the office co-ordinator for the Tiwi Islands Regional Council at Milikapiti, near the most northerly reach of the territory, told AAP the winds were starting to pick up and some people were a "little bit anxious".

Sirens were ready to activate, so the community knew the weather was worsening and it was time to shelter, she said.

The community of about 500 had plenty of food, water and fuel and two extra police officers were on hand to assist.

People had moved to public shelters in the council office and primary school on Friday evening, while others chose to stay at homes deemed safe, Ms Williams said.

As the wind and the rain ramped up in Darwin, most businesses were closed, including major supermarkets.

Conditions are set to ease in the Top End by late Sunday as the system moves to Western Australia.

Cyclone Tracy was the most devastating system to hit Darwin, killing 66 people on Christmas Day, 1974.