A mammoth clean-up was underway in Australia's flood-hit northeast Wednesday after waters began to recede, as the death toll from the storms reached six and thousands of homes were left swamped.

While the worst of the deluge appeared over, many homes remained without power and there were fears of drinking water shortages after rivers swollen by torrential rain from ex-tropical cyclone Oswald breached their banks this week.

Two more people were confirmed dead Wednesday in northern Queensland state after their cars were submerged near Gatton, west of the state capital Brisbane.

They had been missing since Sunday and are believed to be a Malaysian and a Taiwanese in Australia on a working holiday. Their cars were swept off the road near each other as they drove to work at a farm.

Three other men have died in floodwaters and a three-year-old boy was killed when a tree fell on him.

In worst-hit Bundaberg, which was swamped as the Burnett River peaked at a record 9.6 metres (32 feet), authorities moved into recovery mode after the floods inundated about 2,000 homes and 200 businesses.

Queensland Premier Campbell Newman said soldiers were en route to the sugar-farming town where more than 7,500 residents have been forced to seek refuge in evacuation shelters or with family and friends.

"This morning we have 120 soldiers from the Enoggera army barracks in 44 vehicles heading north to Bundaberg," Newman told the Australian Broadcasting Corporation.

More army resources were on standby to help in Bundaberg and surrounding flood-hit communities, he added.

An ABC reporter in the town said petrol stations had run out of fuel while a helicopter and boats were resupplying some of the smaller settlements around the area that remain cut off.

Police said two teenage girls and a 25-year-old man had been charged with looting in the Queensland town of Gympie during flooding there.

While Brisbane escaped the worst of the floods, the deluge damaged water treatment plants and Lord Mayor Graham Quirk said there were concerns parts of the city of two million could run out of water.

"There is still a very real concern that water could run out," he told reporters, although Newman said provisions were in place to supply bottled water to any areas affected.

In New South Wales, a tense night for residents in the northern town of Maclean ended in relief when the Clarence River peaked just below its levee banks at 3.1 metres.

Some 750 people were evacuated as a precaution but were Wednesday given the all-clear to return home, as were thousands evacuated in nearby Grafton, where levees also held to prevent a major disaster.

Acting New South Wales Police Commissioner Nick Kaldas said rescue operations and flood management in the state had gone well.

"It needs to be said that 3,700 requests for assistance in NSW in relation to the flooding, 55 flood rescues and over 1,500 people unfortunately under evacuation orders -- I have to say it has gone very well," Kaldas said.