Brisbane is also on flood alert, with a severe weather warning in place for heavy rainfall in the Capricornia, Central Highlands, Wide Bay, Darling Downs and southeast coast districts.
There have been widespread totals of 90 to 100 millimetres, with higher local falls recorded in areas including Brovinia in the Burnett, which received 239 millimetres.
More than 30 roads have been closed on the Sunshine Coast north of Brisbane.
In the Northern Territory, flooding could persist in Katherine for a week as hundreds of evacuees hunker down to await the all-clear to return home.
The Katherine River was receding late on Sunday after reaching 19.2m on Saturday but plenty more rain is forecast for coming days.
The Daly River, which was at 14.4m late on Sunday, would also continue to rise, Bureau of Meteorology senior officer Jude Scott said.
"The Daly River is expected to continue to rise in the coming days towards the 15 metre or beyond level, and it is expected to remain in major flood for at least the next week," she said.
"We can still, within the active monsoon trough, expect to see showers and storms bubble up that may lead to some isolated totals in excess of 100mm."
Hundreds of people in the Daly River community have been evacuated by helicopter to Darwin, where they are sheltering at the showgrounds.
It is the second time they have stayed there after flooding forced their evacuation in early February.
The flooding is worse this time, with damage to homes and community services expected to be more severe.
Photos showed empty supermarket shelves as flooded highways halted deliveries, although locals said they had been told supplies were expected on Monday.
A boil-water alert has been issued for Katherine by the NT health department, the ABC reports.
Katherine mayor Joanna Holden said the next couple of days would be critical, with more rain forecast.
About 1000 people had been moved to evacuation centres in Darwin, Katherine and Mataranka, she said.
Another 80 people were evacuated from Daly River by helicopter on Sunday after conditions prevented them from leaving on Saturday.
Some schools will remain shut on Monday while they are used as emergency shelters.
Federal and territory governments announced support payments for residents whose houses had flooded.
They ranged from immediate relief payments, capped at $1537 per family, to funds to help replace essential household items such as white goods and furniture.
Flood warnings and flood watches are also in place for much of Queensland.
Moderate to heavy rainfall is forecast across parts of northern, central, and southeast Queensland for the next couple of days as a broad trough draws in deep tropical moisture across the state.
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