Authorities had expected the river to peak in Maryborough above a major flood level of 10.5 metres, impacting about 80 homes on Sunday afternoon, after the remnants of tropical cyclone Seth dumped 600mm on the Wide Bay-Burnett region in two days.
The levee was protecting the CBD until an underground stormwater valve failed just before 2pm, allowing floodwater to surge up through the drains and into the streets.
Police and Queensland Fire and Emergency Services have issued an urgent emergency evacuation order for more than 30 inner-city blocks.
"The Maryborough CBD will be directly impacted by the major flood event," QFES said in a statement.
"The water behind the flood levy has backed up behind the level of the flood barrier.
"The underground valve on the dry side of the levy has been damaged resulting in immediate flooding in the Maryborough CBD.
Anyone in the CBD area has been urged to move immediately to higher ground.
One person has already died in the floods, which came after intense rain pummelled the region on Friday and Saturday.
A 22-year-old's body was found in a submerged ute at Kanigan, north of Gympie, on Saturday.
Police also hold grave fears for a 14-year-old girl swept away while abandoning a flooding car with a 40-year-old man at Booubyjan, near Gympie, in the early hours of Saturday.
The man was found clinging to a tree hours later but police are combing the floodplain for any sign of the girl.
"This is a very, very difficult environment, we are unable to get in there and conduct that search appropriately at the moment," Deputy Commissioner Steve Gollschewski told reporters on Sunday.
"It is going to take some time for us to do that."
Police have received 177 calls for help, while QFES have responded to 51 water-related incidents and made nine rescues.
QFES Deputy Commissioner Mike Wassing urged people not to enter floodwaters or go sightseeing in Maryborough, where a local photographed a bull shark on Saturday.
"I do want to remind people about the dangers of floodwaters," he said.
"We've had the shark in the park, we've got contaminated water, you've seen what can occur with roads in the local areas and how dangerous that is," he said.
"Albeit the rain has stopped, the risk remains."
Meanwhile, a low pressure system in the Coral Sea is expected to intensify into a category one cyclone on Monday morning.
The Bureau of Meteorology says it's likely to cross the coast on Tuesday between Coen and Lockhardt River packing gusts up to 100km/h, abnormally high tides, large waves and heavy rain.
Premier Annastacia Palaszczuk said emergency services were readying for the cyclone, which was expected to be named Tiffany.
"So to all the residents in those areas please be on the lookout, I know that they know how to deal with these events," she told reporters.
"They're very well prepared and we'll be keeping a very close eye on that."
The BoM said there's also a risk the system could further intensify once is passes over Cape York and enters the Gulf of Carpentaria.
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