Blackhawk helicopters are airlifting about 600 flood-affected Bundaberg residents to higher ground as the Burnett River continues to rise.
Police say they are being flown from a temporary evacuation centre at the Oakwood State School to a new evacuation centre near the Bundaberg Airport.
Senior Sergeant Grant Marcus says authorities are preparing for a worst case scenario of a 10 metre flood peak.
"We've moved a large number of people to the Oakwoods State School as a pooling location for our evacuees," Sgt Marcus said.
"The Blackhawk helicopters are commencing the airlift of those evacuees to a new location in the southern area of Bundaberg, where a new evacuation centre has been set up.
"Those people will be housed and taken care of there."
Police have ordered residents to leave their homes in north Bundaberg with a helicopter used to broadcast a mandatory evacuation message.
Emergency Services Minister Jack Dempsey says the Burnett River has broken its banks spilling water into more areas.
Bridges have already been closed and the region is expected to be cut-off when more roads are flooded.
On the other side of the river in east Bundaberg, 140 people have been evacuated from the Liberty Villas retirement village.
Authorities are warning 2,000 homes will be inundated as floodwaters continue to rise.
Around 1,000 homes have already been flooded in the city's north and east, with residents plucked from the roofs of their homes today.
A couple who made it to safety in a boat says some residents are getting desperate.
"[It's] horrible - there's people on rooves yelling out when we were in the boat to come and save them, people lined up for the SES to come and save them.
"People with children [are] sitting on window sills just yelling out."
Community Safety Minister Jack Dempsey says the Burnett River in Bundaberg will reach a flood peak of 9.5 metres tonight affecting a further 2,000 homes.
Businesses in the Bundaberg CBD are also going under.
Warren Mergard from the Salvation Army says the record-breaking flood is already hitting areas that escaped previous natural disasters.
"It's have to be probably a couple of metres higher I reckon than what it was last time," Mr Mergard said.
"We've never had water into this area as far as I know, even back in '1942 or even in 2010-11.
Another two army helicopters have been sent to Bundaberg to help residents stranded in floodwaters.
The State Emergency Service (SES) is assisting with mass evacuations out of the city.
Deputy Mayor David Batts said earlier this morning that residents had begun to realise the gravity of the situation.
"We have hundreds of people if not thousands of people that will be looking for evacuation in the next few hours," Councillor Batts said.
"Those who didn't leave their homes at North Bundaberg during yesterday's evacuations are now being rescued."
The disaster co-ordination centre says helicopters are trying to rescue about 30 people from roofs.
Senior Sergeant Grant Marcus says authorities are doing what they can.
"Swift water rescue is not possible," he said.
"We have three winch-capable helicopters trying to attempt rescues at this point in time."
Residents in urgent need of rescue have been told to climb onto their roofs.
River levels have already surpassed the 1942 record and are a metre higher than in the 2010 flood.
Meanwhile, hundreds of cattle have been washed away in flooding in the North Burnett region north west of Bundaberg.
Mayor Don Waugh says the flood damage in the region is devastating.
He says homes have been inundated and there is widespread citrus crop damage at Gayndah.
Councillor Waugh says a large dairy farm at Mundubbera has been wiped out.
"That dairy property has a milking operation, milking 400 head of cattle that has been totally inundated," he said.
"The cattle [have been] washed away and there's nothing left."
© ABC 2013
15:01 EDT A cyclone and potential cyclone are expected to bring heavy rain to north Queensland and the Gulf country in coming days.