Territory authorities declared an emergency for communities where the upper Victoria River reached major flood levels on Wednesday.
"Earlier predictions were that the river would reach moderate flood level, however that has now been exceeded," NT Police Commander Daniel Bacon said.
About 700 people were to be relocated by air to Katherine and then driven by bus to temporary accommodation in Darwin.
Cmdr Bacon said access roads to the communities had been cut, with the community of Daguragu isolated by floodwaters for two days.
Residents of Daguragu were evacuated to the community of Kalkarindji ahead of further inundation expected on Wednesday night.
The Victoria River at Kalkarindji is rising above the major flood level of 14m, and likely to peak near 17.3m on Wednesday evening.
The town, located about 550km south of Darwin, had 99mm of rain by 6am on Wednesday morning.
The Bureau of Meteorology has warned residents of flash flooding with six-hourly rainfall totals of up to 140mm throughout the day.
"A decision has been made for the safety of the residents to evacuate," Cmdr Bacon said.
Authorities have urged people in the area to avoid unnecessary travel to allow for the safe evacuation to take place.
The affected communities are in the Gregory region, southwest of Katherine.
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