"Severe Tropical Cyclone Megan is beginning to impact the southwestern Gulf of Carpentaria coast," the Bureau of Meteorology advised at 8pm (ACST) on Sunday.

The weather system has intensified into a low-level category three with a "moderate chance" of developing into a category four when it makes landfall, the Bureau said.

"It does have enough time that it can strengthen," the Bureau's Shenagh Gamble said.

"... If this system slows down, it is in a favourable enough environment that it can strengthen to a category four tropical cyclone," she said.

"The very destructive core of severe Tropical Cyclone Megan is expected to cross the coast during Monday and those very destructive winds will be gusting up to 220 kilometres per hour.

"Destructive winds of up to 125 kilometres per hour can be expected in the south-west Gulf of Carpentaria from Nathan River around to the NT/Queensland border this afternoon or overnight.

"We are currently observing sustained winds of 120km/h gusting to 165km/h around the centre of this tropical cyclone."

Evacuations from Borroloola to Darwin will commence at 7am on Monday, March 18, with up to 240 elderly and vulnerable residents set to be flown from the Borroloola Airport to Darwin.

A further 520 residents will also be evacuated from the Borroloola Airport to the Glencore McArthur River Mine then on to Darwin.

Tropical Cyclone Megan has already hit the southwestern Gulf of Carpentaria coast hard.

Groote Eylandt received more than 400 millimetres of rain in just 24 hours, and by 9am on March 17, a whopping 680 millimetres of rain had fallen within 48 hours, causing flooding across the island.

Meanwhile on Galiwin'ku, off the Nhulunbuy coast, locals lost power and water supply intermittently on Friday, with some residents left without essential services for 48 hours.

The Bureau of Meteorology advises the current Cyclone Warning Zone ranges from Alyangula (Groote Eylandt) in NT to Mornington Island in Qld (not including Mornington Island), extending inland to Borroloola, McArthur River Mine, and Robinson River, but not including Ngukurr.

"It's quite a large tropical cyclone, taking up around one third of the Gulf of Carpentaria area," Ms Gamble said.

"We (are expecting) to see widespread heavy totals of 150 to 200 millimetres of rain, but particularly around the core of this system ... we could see rainfall totals of around 300 to 400 millimetres.

"We have a flood watch current for much of the eastern parts of the NT including the Barkly catchment area."

Police can be contacted at the Borroloola Police Station in the morning if needed on 8975 8770.

On Sunday night, there were wind speeds of 130km/h with gusts of up to 185km/h as it moved south through the gulf towards land.

The warning zone for the system stretches hundreds of kilometres from Alyangula on Groote Eylandt in the NT to the Queensland border and inland to Borroloola, the McArthur River Mine and Robinson River.

"It's quite a large tropical cyclone, taking up around a third of the Gulf of Carpentaria area," Ms Gamble said.

The Bureau said the cyclone would have a "very destructive core" when it makes landfall on Monday, with wind gusts of up to 220km/h expected as it crosses the coast between the Nathan River in the NT and the NT-Queensland border.

Rainfall totals exceeding 300 or 400mm are forecast for the centre of the cyclone while widespread rainfall between 150 to 200mm is forecast for surrounding areas.

Coastal residents between Nathan River and the border are specifically warned of a dangerous storm tide.

"There is a very dangerous storm tide associated with this system and tides are significantly higher than the normal high tides," Ms Gamble said.

Flood watches are in place for the Carpentaria, north western parts of the Top End, Arnhem, Barkly and eastern Daly districts.

NT Police Superintendent Sonia Kennon said people who are considering evacuating themselves, needed "a capable vehicle" as there was already damage to the Carpentaria Highway.

"If you are leaving the community, please ensure that you go to the local police station.

"Advise and leave your name, persons in the vehicle, registration of the vehicle, contact details and address of where you're going to be locating yourself to," Supt Kennon said.

"This is to ensure that we can follow up on you."

Residents are urged to prepare now before the cyclone makes landfall by securing loose items on their property, storing water and ensuring they have stocked up on food.

"When the tropical cyclone does arrive, we need you to take shelter inside. Stay indoors until all clear is given by the authorities," Supt Kennon said.

Communities outside the tropical cyclone warning zone could still feel the impacts of wind and rain, with a severe weather warning for heavy rainfall issued in the East Arnhem district.

The weather system is expected to return to a tropical low as it heads further inland on Tuesday and Wednesday, prompting the bureau to issue flood watches for further river rises across the territory.

But once over land, Megan will weaken and track west through the Northern Territory as a tropical low.

- with Australian Associated Press