Flooding has cut off access to the Aboriginal community of Jilkminggan, south of Katherine, prompting an operation to evacuate residents.
NT Police said around 250 people were stranded when rapidly rising waters surrounded the community on Thursday.
The service said the local emergency committee took the decision to evacuate as a precaution.
"Access roads to Jilkminggan have been cut and the community is now surrounded by water — inundation is predicted in the near future," Regional Controller Acting Assistant Commissioner Travis Wurst said.
"A decision has been made for the safety of the community to evacuate today."
Police used boats and buses to move people to nearby Mataranka, with residents staying overnight in the town hall.
"The evacuees will be looked after in Mataranka tonight, and a decision will be made tomorrow or coming days whether they will be relocated, depending on the situation," Acting Assistant Commissioner Wurst said.
A moderate flood warning was issued for the Daly River on Thursday afternoon but no evacuation orders are in place for the Nauiyu community, which has been on flood watch all week.
The Bureau of Meteorology said no significant rainfall was recorded during the day in the Lower Daly catchment but warned water from upstream rivers was still moving downstream.
A final flood warning was issued for the Katherine River where the bureau said levels were continuing to ease below minor flood levels.
