Residents in one of the Aboriginal communities, Daly River, were forced to flee for a second time within weeks as water levels rise across the region.
Bussed to emergency accommodation at a Darwin showgrounds pavilion in early February, the same people were this time flown out by helicopter.
Around 200 members of inundated Palumpa were also being evacuated to a Darwin stadium by six fixed-wing aircraft on Saturday.
The heavy rain and a rising river have also put the major Northern Territory town of Katherine under threat as waters surpass major flood levels.
Shenagh Gamble of the Bureau of Meteorology said the Daly River catchment had received "extraordinary rainfall" associated with a tropical low and the river would likely continue rising over the next week.
"So we do expect the flood levels at the Daly River community to far exceed previous flood levels," she told reporters in Darwin on Saturday.
The Katherine River, meanwhile, continued to rise and was expected to peak at 19.2 metres on Saturday night and stay above major flood levels into Sunday.
NT Chief Minister Lia Finocchiaro said the helicopter evacuation of about 400 people from Daly River would involve seven choppers.
They were being flown to the town of Batchelor before being bussed on to Darwin showgrounds again.
Ms Finocchiaro said it was a difficult time.
"They've just been repatriated back home and are now facing a significant flood again and the bureau is expecting water levels to increase over the week," she said in Darwin.
In Katherine, 377 people were in emergency shelters and sandbags were being made available.
Acting Police Commissioner Travis Wurst said the majority of the CBD was still dry apart from some seepage via a drainage system.
He said a helicopter would winch to safety 10 people isolated by floodwaters in Palumpa where a number of houses had been inundated and water and sewerage systems impacted.
It could be some time before they could return to homes which had to be deemed safe by assessment teams, with power, water and communications restored, he said.
"There's no point sending people back into a community that is not ready to receive them and that is going to take some time."
Authorities were working on making the evacuees as comfortable as possible while in Darwin, Mr Wurst said.
In Katherine overnight, six people were rescued after they were trapped in their houses by rising waters.
The town remains cut off from the Stuart Highway and could be for an extended period.
Its hospital was closed on Friday, with some 20 patients flown to Darwin.
In Queensland, almost all the state's coastline is under flood alert as a tropical low pushes inland.
The Herbert and Daintree rivers in the north were continuing to flood after massive rainfall in the previous 24 hours, Bureau of Meteorology senior meteorologist Dean Narramore said.
There's not much short-term relief in sight as most of the state should prepare for the soaking to continue, he said.
"We're likely to see showers, rain and thunderstorms spread right across northern and eastern Queensland over the weekend.
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