The death of a little boy hit by a falling tree has taken Queensland's flood toll to four, as the provincial city of
Bundaberg remains in the grip of its worst-ever flood.

A family is grieving the loss of the three-year-old who died in hospital overnight after he and his mother were struck by a falling tree in Brisbane's north on Monday, the Australian Associated Press (AAP) reports.

Three men have also died in floodwaters.

The city of Bundaberg is of most concern on Tuesday, with 2,000 people in evacuation centres and 2,000 properties affected by flooding.

There are ongoing concerns that houses could be swept from their stumps as torrents of water course through swathes of the city.

Overnight, a fleet of 14 helicopters rescued more than 1,000 people from Bundaberg's northern suburbs, and missions are expected to continue on Tuesday, said APP.

"There may still be people in there and we have to get them out," Queensland Premier Campbell Newman said on Tuesday morning.

Planning is also well-advanced for the evacuation of more than 100 patients from the Bundaberg hospital, amid concerns it could lose power. They will be flown to Brisbane hospitals.