Hundreds of residents bussed from Daly River to emergency accommodation at a Darwin showgrounds pavilion in early February will this time be flown out by helicopter.
Around 200 members of the flood-hit Aboriginal community of Palumpa were also being evacuated to a Darwin stadium by fixed-wing aircraft on Saturday.
As the Northern Territory cops a drenching, almost all of Queensland's coastline is under flood alert as a tropical low continues to move inland.
Heavy rain across a number of NT catchments has led to rivers and creeks rising rapidly, with the town of Katherine under threat as waters reach above 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 was expected to 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 reach a peak of 19.2 metres on Saturday night and stay above major flood levels into Sunday.
NT Police Incident Controller Shaun Gill said emergency authorities were organising a helicopter evacuation of about 400 people from the Daly River community starting on Saturday for transfer to the Darwin showgrounds pavilion.
In Katherine, sandbagging was under way and about 200 people were in emergency shelters in the town.
"The message for Katherine people is that if you want to go into shelter, now is the time to act. The flood conditions are only going to get worse in the short term," Commander Gill said.
A levee system designed to mitigate flooding has also been put in operation for the first time.
About 200 residents in Palumpa were being evacuated by fixed-wing aircraft to be housed at a stadium in Darwin on Saturday, Commander Gill said.
In Katherine overnight two rescues were made of people trapped in their houses by floodwaters.
Commander Gill confirmed some homes were flooded, the main street was starting to be impacted, the Stuart Highway was cut and the river bridge was expected to go under on Saturday afternoon.
Katherine Hospital was closed on Friday, with some 20 patients flown to hospital in Darwin.
In Queensland, almost all of the state's coastline is under flood alert as a tropical low continues inland.
The Herbert and Daintree rivers in the north of the state are continuing to flood after massive rainfall in the last 24 hours, Bureau of Meteorology senior meteorologist Dean Narramore said.
Alligator Flats, near Gladstone, recorded 212mm while most of northern inland Queensland saw falls of between 50 and 150mm.
There's not much short-term relief in sight as most of the state should prepare for the soaking to continue, Mr Narramore said.
"We're likely to see showers, rain and thunderstorms spread right across northern and eastern Queensland over the weekend.
"Widespread areas ... getting 50 to 100 millimetres (is probable) with a stretch of more 100 to 200 millimetres possible around the (tropical) low."
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