Prime Minister Julie Gillard says 100 defence personnel are being deployed to Bundaberg to assist with the flood emergency.
Already four Black Hawk helicopters and two Hercules C-130 planes are being used in rescues and evacuations.
More than 2,000 residents spent the night in evacuation centres as the Burnett River continues to rise.
The Bureau of Meteorology says it will peak at nine-point-six metres this afternoon, slightly higher than the previous prediction of 9.5 metres.
Premier Campbell Newman met with the local disaster management group in Bundaberg this morning.
"There's clearly a lot of things we have to do given what we've got," Mr Newman said.
More than 40 patients from the Bundaberg Hospital were flown to hospitals in Brisbane, Hervey Bay and the Sunshine Coast this morning.
More will follow this afternoon.
It is feared houses could be washed away by the force of floodwaters and the local council is predicting entire suburbs will be swamped.
Water is encroaching on the city's hospital, and 10 critically ill patients were flown to Brisbane last night.
Medical transport hubs have been set up in the Bundaberg and Brisbane Airports to help with the transfer of 130 patients today.
Wide Bay Health chief executive Adrian Pennington says the defence force is helping.
"With the support of everybody, we are ready to go," Mr Pennington said.
The Royal Flying Doctor Service and CareFlight are also expected to take part in the operation.
Mr Pennington says the hospital's emergency department will remain open for now.
"We have located a second ED facility which we will open later today if - and only if - the water levels raise to such a level that that the power would be lost to the hospital."
Yesterday a dozen helicopters including defence force Blackhawks were used to rescue about 1,000 stranded residents in a massive air rescue operation.
Those plucked from rooftops included a pregnant woman and her family.
Melissa Smith was among other residents winched to safety.
She says the damage to Bundaberg North homes is heartbreaking.
"There's debris everywhere, the trampolines are everywhere, all the kids stuff is everywhere - it's just gone," she said.
Janine Cooney-Law was rescued from her home which was rapidly going under water.
"We saw water coming up all around the sides of it," she said.
Ms Gillard says relief payments are also being made available throughout the state to help those effected.
"What we've done already, working with the State Government, we've commenced what's called the natural disaster relief and recovery arrangements,' Ms Gillard said.
"They're active in 46 local government areas."
© ABC 2013
23:46 EST The Australian Government has committed an extra $35 million of aid to help with the cyclone recovery effort in Vanuatu.