A building is surrounded by flood waters in Londonderry on the outskirts of Sydney, Australia, on Thursday. AP

Emergency services ordered some Sydney residents to prepare to flee as heavy rainfall barrelled down Australia's east coast, burying towns in floodwater, killing 13 and putting hundreds of thousands at risk.

Around 500,000 people in Sydney and its surrounds had by Thursday been told to evacuate or prepare to flee floodwaters as torrential rain lashed an extraordinarily long stretch of the Australian east coast.

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A week-long torrential downpour has swollen rivers and reservoirs past bursting point, causing chaos in an area 800 kilometres (500 miles) long.

From Brisbane to Sydney, more than 30 evacuation warnings are in place and several dams are overflowing, with some near Sydney under threat of bursting.

This handout photo shows an aerial view of a flooded area in New South Wales. AFP

Rivers were rising in Australia’s most populous city, home to 5 million, with New South Wales’ State Emergency Services Minister Steph Cooke warning of "treacherous weather conditions” over the next 24 hours.

Terrified residents have sought refuge on higher ground, in make-shift evacuation centres, or by clambering into attics or onto rooftops praying for rescue by boat or helicopter.

In the hard-hit town of Lismore, Lucy Wise said the floods came much quicker and much higher than expected.

This handout photo shows an aerial view of the flooded northern New South Wales town of Woodburn. AFP

"The rain just wouldn't stop and the water was just coming up so fast" she told AFP.

Australia’s Bureau of Meteorology warned of life-threatening flash flooding and damaging winds with peak gusts in excess of 90 kilometers (56 miles) an hour.

Major flooding was expected along several rivers in and around Sydney. Dozens of suburbs were on high alert.

The State Emergency Service issued evacuation orders to 200,000 residents and evacuation warnings had been sent to another 300,000.

Residents look over a flooded road near Windsor on the outskirts of Sydney, Australia, on Thursday. AP

New South Wales Premier Dominic Perrottet urged residents to take the orders seriously.

"We do believe that things will get worse before they get better," Perrottet said.

Minor flood warnings were also issued for coastal communities as far as 200 kilometres (120 miles) south of Sydney.

Floodwaters were also rising in Brisbane, Australia’s third-most populous city 730 kilometres (450 miles) north of Sydney, as severe thunder storms struck.

Hailstones 5 to 6 centimetres (2 inches) wide pounded the town of Inglewood, 270 kilometres (170 miles) southwest of Brisbane, early on Thursday, the Bureau of Meteorology said.