Everyone in the affected area, including the community of Daly River, has been safely evacuated north to Darwin but their homes are inundated.
"There is not a building in Daly River that is not under water, many of which are under water to the roof," Northern Territory Chief Minister Lia Finocchiaro told reporters on Saturday.
"We have to let that river go down before we can take any further steps."
Levels along the waterway, one of the territory's few that flows year-round, are peaking above those set three decades ago.
Moderate rain forecast for the area over the next few days means it will stay that way well into next week.
The Bureau of Meteorology is closely monitoring the situation and will issue fresh warnings as required.
Wet weather has devastated the NT, swamping remote communities and affecting Darwin's water supply.
The flooding in Katherine is the worst in almost 30 years, with crocodiles sighted around town.
The total number of homes and businesses affected there is still being tallied but the Insurance Council of Australia has declared it a significant event.
The NT's Emergency Operations Centre remained in response phase, Ms Finocchiaro said.
"We have as of today, about 621 people still in evacuation centres right across the Top End.
"That includes Darwin, Katherine and in Mataranka.
"We will be planning to repatriate people home, obviously as soon as possible, but it has to be safe and so we working through that now."
A minor flood warning for the Katherine River has been downgraded, while flood watch alerts are active for Central and Western Inland Areas.
One of the biggest welfare responses the territory had undertaken was being rolled out, Ms Finocchiaro said.
Some 1275 prepaid emergency debit cards have been issued, totalling $1.15 million in value.
"More than 1100 payments have already been made and it equates to about 25 per cent of Katherine's population receiving payments," she said.
Authorities are also waiting to hear whether ADF support might be forthcoming for the town.
In western Queensland's channel country, a major flood peak along the Georgina River has passed through Marion Downs and is approaching Eyre Creek, the bureau said on Saturday.
Significant renewed river level rises were occurring at Bedourie and Glengyle, while showers and thunderstorms were forecast throughout the region over the next few days.
The disaster has so far claimed the lives of two backpackers from China who drove off a bridge on their way from Brisbane to the rain-hit North Burnett region.
Another man is missing after falling from a houseboat in the Burnett River near Bundaberg on Friday.
Bundaberg is one of the communities in recovery mode after more than 350 Queensland homes and businesses were inundated.
A string of rescues have been executed across the state, with footage released on Friday showing a woman in her 80s eagerly receiving help before being ferried to safety as Chinchilla locals evacuated.
Attention has turned further west to Longreach, where emergency alerts were issued ahead of the town's first major flood since 2000.
It was set to be affected by "pretty big" flooding on the weekend or early next week, the Bureau of Meteorology said.
"We are well prepared but it doesn't avoid the fact some houses will have water go through them," Longreach Mayor Tony Rayner told the ABC.
As of Friday afternoon, flooding had closed more than 450 Queensland roads, claimed 250 livestock and damaged or ruined over a thousand fences.
The federal and state governments have activated disaster recovery grants worth up to $75,000 and low interest loans of up to $2 million for affected primary producers.
Emergency payments are also being made available of $180 for individuals and up to $900 for families of five or more for essentials like food, clothing and medicine.
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