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The Northern Territory Police Commissioner says a "one-in-100 year" flood is coming to the remote community of Borroloola, with the Australian Defence Force attempting to evacuate vulnerable residents before dark on Wednesday evening.
Police Commissioner Michael Murphy said updated modelling following heavy rains associated with ex-Tropical Cyclone Megan now predicted the McArthur River at Borroloola to reach 18 metres – three metres above the river's recorded major flood peak in 2001.
Previous modelling had drastically underestimated the impacts of rainfall on the river, Mr Murphy said, with authorities having planned for a 15.3 metre peak.
Mr Murphy said a peak of 14.9 metres represented a major flooding event at the river.
"A one-in-100-year flood is really serious," he said.
"We're taking it incredibly seriously and we're doing everything we can to ensure the residents of Borroloola are safe.
"It's absolutely significant, it probably just demonstrates the change in environmental conditions we're facing … and increased flood levels."
Plans to evacuate Borroloola were cancelled earlier this week, but by Wednesday afternoon another evacuation was ordered for Borroloola by the NT government, with authorities expecting to relocate about 250 residents.
Mr Murphy said two residential areas of Borroloola, Garuwa and Yanyawa, were home to about 350 residents and would be inundated.
"We're working incredible hard now to ferry the Garuwa community across Rocky Creek in boats and get them to the airstrip," he said.
"We're working incredibly hard with the Australian Defence Force."
Late on Wednesday afternoon Mr Murphy said a Hercules aircraft was loading 40 passengers for evacuation, with two more Hercules planes on the way to Borroloola pegged to evacuate about 100 residents each to Darwin before nightfall.
The planes, he said, were carrying four tonnes of food and water to be distributed to residents who remained in Borroloola.
"The pilots and the ADF, they will probably have to look at last light to stop flying, but they can take off, so we’re just working against the clock to get people on board these flights and get them to Darwin," Mr Murphy said.
The Borroloola residents are being evacuated to Foskeys Pavilion and Marrara Stadium, authorities said.
Mr Murphy said emergency services were working with local health and welfare groups to prioritise evacuees.
"And we've got 78 medically-vulnerable people in the community, so we're working through that health area to see who may move," he said.
Evacuation plans for about 700 residents from Borroloola were suspended on Monday after deteriorating weather conditions prevented two Australian Defence Force planes from landing safely.
Mr Murphy said the decision to once again evacuate residents came after the Bureau of Meteorology, which he said had been dealing with "connection issues with some of their meters", received a revised forecast from the McArthur River Mine nearby.
"We are reliant on the information from the Bureau [of Meteorology] and the bureau modelling was putting [the flood peak] 15.3 metres," he said.
"As the days progressed [the bureau] had some intermittent connection issues with some of their meters, they reached out to the McArthur River Mine, and they provided some more information which indicated the volume of water was much more significant than originally thought.
"And as soon as we've gotten that information [emergency service authorities convened] … and this is the action we are taking from that."
Earlier this week Borroloola residents criticised the way the failed evacuation of the community was handled by authorities, accusing the NT and federal governments of putting locals at risk by being too slow to enact the plan to fly them out.
NT Police Minister Brent Potter defended his government's decision to cancel the evacuation, which he said would have been "too risky" to facilitate at night.
Mr Murphy said flooding could be expected across the Top End in the coming days as the weather system tacked from the Gulf of Carpentaria to West Australia.
"We'll see 50-100 millimetres [in parts] … so we'll see localised flooding and roads being cut off in communities," he said.