Heavy rain continues to batter the Northern Territory as a deep tropical low tracks slowly east across the Top End.

Hundreds of people are being evacuated from remote communities where floodwaters threaten to isolate residents.

Heavy rainfall and potential flash flooding are forecast for parts of the Gregory, Tanami, Barkly and Carpentaria districts on Thursday.

The rain is expected to spread east across the Barkly, with six-hourly rainfall totals between 90mm and 140mm possible.

Intense storm cells and damaging wind gusts are forecast for the area south of Kalkarindji to Renner Springs.

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 levels. 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 residents of Daguragu evacuated to Kalkarindji ahead of further inundation expected on Wednesday night.

The Victoria River at Kalkarindji surpassed the major flood level of 14m, and was at 16.02m and still rising on Thursday morning.

The town, about 550km south of Darwin, recorded the highest rainfall of 133mm to 9am on Wednesday.

The Bureau of Meteorology has warned residents of flash flooding across the Top End in locations including Tennant Creek, Elliott, Kalkarindji, Lajamanu, Renner Springs and Mallapunyah.

Authorities have urged people in the area to avoid unnecessary travel to allow for a safe evacuation.