Residents in a remote Northern Territory fishing community will be evacuated over fears a major river will flood.

Emergency crews announced a partial evacuation had been ordered for Borroloola after modelling showed the McArthur River was forecast to hit a peak of up to nearly three metres higher than first thought.

Territory Controller commissioner Michael Murphy said the latest forecast showed Yanyula, Garrawa and parts of Borroloola were likely to be inundated by flood waters.

“At this level, several homes and homeland communities will be inundated, but the Borroloola town centre, including the shop and school, will remain above water level,” Murphy said.

“A one-in-100-year flood is really serious and we’re taking it incredibly seriously and we’re doing everything we can to make sure the residents of Borroloola are safe.”

The dangerous flooding follows this week’s Tropical Cyclone Megan, which lashed the town of about 700 people. An Australian Defence Force effort to evacuate the town on Monday before the cyclone arrived had to be called off, leaving residents to ride out the storm in the remote town.

Borroloola suffered only minor damage from Megan, but the flooding that has followed presents a new threat.

Multiple RAAF planes headed to Borroloola late on Wednesday, carrying with four tonnes of food and water.

Their return flights were to bring 130 people to Darwin, where they were to be accommodated at Foskeys Pavilion and Marrara Stadium.

“Those 130 will be identified by local authorities and health staff on the ground, based on their medical and care needs and on the likelihood of their homes being damaged by floodwaters for an extended period,” Murphy said.

Evacuation flights were to depart every 40 minutes until dark on Wednesday, each carrying up to 70 people.

Residents were also told they might need to move to higher ground in the town centre, if flights were unable to land safely in Borroloola.

“The town centre itself will remain dry. We are working on a plan for a higher than forecast peak and the community will have access to food and shelter until the crisis is passed,” Murphy said.

-AAP