Fitzroy Crossing and dozens of Indigenous communities have already been hit by record flooding and WA's only road transport route to the north of the state is likely to be cut for months after a major bridge suffered significant damage.
"People are suffering ... people are scared," WA Emergency Services Minister Stephen Dawson said.
Fitzroy Crossing's supermarket and homes have been inundated and only a few of the town's streets remain above the murky floodwaters, with people, livestock and wildlife clambering for the remaining dry ground.
The evacuation centre in the town of about 1500 was at capacity on Wednesday, as authorities commandeered boats and helicopters to transport people to safety.
Another evacuation centre was being set up, the federal government said on Thursday.
Two Australian Defence Force C-130 Hercules aircraft, which can carry 80 passengers, and a C-27 have been deployed to the region to join the fleet of aircraft carrying out evacuations and deliveries of urgent supplies.
Federal Emergency Management Minister Murray Watt said the ADF planes have had difficulty getting into the area because of the weather.
"But we are exploring some other options to provide that support," he told ABC Radio on Thursday.
"In the meantime, the Western Australian government has been able to source some of its own aircraft and relocate people."
Authorities are particularly concerned for around 50 remote Indigenous communities outside of Fitzroy Crossing, comprising several hundred people.
"We're concerned about the risk of isolation, potentially for weeks, for those communities," Mr Watt said.
"There will be people who don't necessarily need to be relocated, but will have some issues obtaining food, vegetables, all sorts of other things and it will be important to make sure that we can resupply those kinds of communities."
The Fitzroy River peaked at the town late Wednesday, reaching a record 15.8 metres, Emergency WA confirmed on Thursday.
About 60,000 cubic metres of water per second has been flowing down the swollen waterway, which snakes its way across the Kimberley to the coast at Derby, north of Broome.
"It's one of the highest flow rates we've ever seen in an Australian river," meteorologist James Ashley said.
"The amount of water moving down the Fitzroy River in a day is about what Perth uses water-wise in 20 years."
Authorities have warned people in Broome and Derby to prepare to be cut off as early as Thursday, with ex-tropical cyclone Ellie expected to dump up to 200mm of rain in the area, causing roads into the towns to be flooded.
The weather system is hovering close to Broome where it is forecast to remain before moving slowly east back across the Kimberley towards the Northern Territory later in the day.
Mr Dawson said pastoralists and livestock had also been impacted significantly by the flooding.
"Until the floodwaters start to recede it won't be possible to undertake a full assessment of damage and stock losses in the region," he said.
"This is very distressing for the community."
Meanwhile, major flooding continues in the western NSW town of Menindee, where the Darling River was holding steady at around 10.2m on Wednesday but could rise to 10.7m from Thursday, above the 1976 flood record of 10.47m.
