Around 300 people from Daly River are being housed at a pavilion at the Darwin Showgrounds but it could be many days before they can return home.
Incident controller Gavin Kennedy said on Wednesday hopes of flood levels falling overnight were dashed when a thunderstorm added to flows and increased inundations in the township.
"There are now quite a number of houses where the water is ankle deep ... it's likely by the end of the day they'll be into double figures," he told reporters in Darwin.
Controller Kennedy said it was not expected that water, electricity and the sewerage system would need to be switched off but the town's roads and airstrip were almost completely underwater.
Police on site are flying drones several times a day to monitor the flooding in the township about 220km southwest of Darwin.
A return time for evacuees depended on the waters receding and assessment teams getting in to determine if all was safe, Controller Kennedy said.
The Bureau of Meteorology had earlier expected the river to peak at 4.1 metres on Tuesday before waters started to recede.
Bureau senior officer Jude Scott told reporters the flooded river was now expected to peak later on Wednesday at around 14.3 metres before slowly receding in coming days.
It was expected to drop below the major flood level overnight on Thursday then remain above the moderate flood level of 13.1 metres until early next week.
Heavy rain in parts of Central Australia in recent days has also filled the usually dry Todd River in Alice Springs, sent waterfalls down the flanks of the rock at Uluru and cut off remote communities, but pastoralists are pleased.
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