Helicopters plucked dozens of stranded Australians to safety in dramatic rooftop rescues Monday as severe floods swept the northeast, killing three people and inundating thousands of homes.

The body of one man carried away by rising waters was found in the Queensland state capital Brisbane and another further north at Gympie, following the earlier discovery of an elderly man who died near the city of Bundaberg.

A pregnant woman and her three-year-old son were hospitalised after a large tree fell on them as they were walking Monday morning in Brisbane. They were reported to have head injuries, with the child in critical condition.

Queensland Premier Campbell Newman announced that an acute emergency was unfolding in Bundaberg, home to about 50,000 people some 360 kilometres (220 miles) north of Brisbane, with people scrambling to get out as the river hit a record peak.

One family zipped their infant son into a waterproof bag to be winched to safety by helicopter as floods surrounded their car on Sunday at Biloela, west of Bundaberg.

Newman said authorities were now in "uncharted territory", with debris-laden floodwaters roaring through the town at such speeds that evacuations by water were no longer viable. There were fears homes could be ripped from foundations.

More than 2,000 houses had flooded and "many thousands" of people were affected, he said, with a "significant number" of people soon to be trapped.

Some 60 patients at the local hospital were being shifted to upper floors.

"We are at a point where we've never seen floodwaters like this before," Newman told reporters.

"We're very concerned that the velocity of the water and the rise in water levels means that literally houses, particularly in North Bundaberg and maybe other locations, could be swept away. This is a very real prospect."

Fourteen helicopters including two army Black Hawks would fly rescue missions until nightfall and Newman said the government was scrambling to find extra aircraft.

"We've got to pull all stops out to do this before it gets dark," he said.

Thousands have evacuated their homes across Queensland with flood warnings for most of the state's rivers as ex-tropical cyclone Oswald pushes into neighbouring New South Wales, bringing high winds and heavy rains.

Pounding surf whipped up huge ocean froth on the Gold and Sunshine Coast regions, with foam up to one metre deep in some areas of the shore.

Prime Minister Julia Gillard said the "wild weather had broken a lot of hearts", with some Queensland residents experiencing their third flood in two years, including the devastating 2011 inundation which killed 35 people.

"As this weather moves into New South Wales can I reiterate to everyone, it is very important you keep yourself safe," said Gillard.

"We have seen three fatalities and... we have got grave concerns for a number of others."

Floodwaters were rising in Brisbane, home to some two million people, though Newman said the Brisbane River was expected to peak seven metres lower than in 2011, when flooding brought the city to a standstill for several days.

Rural towns were isolated by floodwaters in neighbouring New South Wales state, where hundreds of millimetres of rain and strong winds were expected in the coming hours, including in Sydney.

Cyclones and floods are common in Australia's northeast during the warmer summer months. A series of huge storms wreaked havoc across Queensland in early 2011, devastating large agricultural districts and major coal mines.