Hundreds of residents have been evacuated from a remote Northern Territory town after the area was lashed by ex-Tropical Cyclone Megan, as rising floodwaters left 200 mine staff stranded at work.

Phone towers are down in the town of Borroloola after the region was hit hard by severe weather during the week.

The defence force had evacuated more than 370 residents by Friday after the category three system flooded homes.

About 700 people remain in the town and 100 are in shelters, according to Northern Territory Police Superintendent Sonia Kennon.

She said authorities were aware of concerns about the partial evacuation, including from people whose houses were flooded, but stressed it happened quickly and vulnerable residents were removed first.

“It’s just a matter of trying to do the best that we can in the time that was permitted,” Kennon told reporters on Friday.

She said there was intention to evacuate other communities but contingency plans were in place.

Aircraft carrying supplies for those who remain in Borroloola were expected to land on Friday afternoon.

Nearby McArthur River mine is returning to normal operations after 200 people were stuck at the mine on Wednesday night.

Rising floodwaters cut off an internal road connecting the mine and workers’ accommodation, a Glencore spokesperson confirmed.

They said all workers were safe and had access to food, showers and power.

A temporary road has been built and a helicopter used to move people between the two locations.

Mobile phone connectivity has been wiped out across the area after two base stations lost power.

Telstra regional general manager Nic Danks earlier on Friday said the telco’s stations at Borroloola and nearby McArthur were out of action. 

“Our equipment in these remote locations are primarily powered by solar panels and the poor weather is limiting their ability to recharge the batteries,” he said.

It is unclear when the stations will be brought back online but the company promised to get crews into the area as soon as possible.

“With roads closed, access to the area is by helicopter only at the moment and they are currently in high demand,” Danks said.

“The high water levels in the area will also pose challenges for our crews to safely land in near proximity to our sites.”

He said about 400 fixed-line services were also offline at Bing Bong, Mallapunyah and Borroloola.

The Bureau of Meteorology believed major flooding had occurred at the McArthur River, but said no recent river level observations were available as of Friday morning.

“Over 500mm fell across coastal parts of the southwest Gulf of Carpentaria with the crossing of the system,” meteorologist Sarah Sculley said.

“Now these huge volumes of water are making their way downstream.”

Ex-Tropical Cyclone Megan formed off the territory’s eastern coast and has moved west to the border with WA, bringing thunderstorms to the Kimberley region.

A severe weather warning has been issued for the Tanami district in the centre of the Northern Territory and up to 120mm could fall during the rest of Friday, Scully said.

The wild weather has triggered flood watches for large parts of central and northern Australia, including Queensland.

Tropical Cyclone Neville remains off the WA coast but is not expected to affect the mainland.

It is located about 900km southwest of Christmas Island and is tipped to peter out as it moves west.

Two other cyclones, Lincoln and Kirrily, have battered northern Australia this year.

–AAP