Extreme weather has lashed south-east Australia, causing scores of homes to flood in regional Victoria and forcing the cancellation of 100 flights at Sydney Airport.

Properties in Newry, Gippsland, in Victoria’s east, were inundated on Thursday morning as huge rainfall totals since Tuesday caused rivers and lakes to swell.

Forecaster Weatherzone warned that flooding was also expected to increase in other parts of Victoria in coming days.

By Thursday afternoon, it was feared that 130 houses could be inundated to above their floorboards in towns downstream of Lake Glenmaggie in Gippsland, including at Newry.

There have been falls of more than 100 millimetres in north-east Victoria since Tuesday, with the heaviest in East Gippsland and south-east NSW.

In NSW, extreme winds wreaked havoc and caused flight cancellations at Sydney Airport on Thursday morning.

Only one runway was in use due to the gusty conditions. More than 100 domestic departures and arrivals were cancelled as the runway restriction meant nearly half of all scheduled flights could not operate.

Across NSW, wind-damaged roofs and fallen trees sparked most of the 291 calls to SES volunteers in the 24 hours to midday Thursday, including 113 incidents in the state’s north.

Victorian residents prepare for the onslaught. Photo: Facebook (Darren Chester MP)

In Victoria, Gippsland MP Darren Chester said the rain had stopped but “there’s still plenty of water coming down the Macalister River”.

Flooding can be expected to increase in coming days, with numerous moderate and major flood warnings in place for rivers.

Earlier, thousands of Victorians were told to evacuate as rising rivers broke their banks, just days after the region was ravaged by bushfires.

People in Tinamba, Tinamba West, Newry, Mewburn Park, Bellbird Corner, Riverslea and Maffra were told to leave immediately on Wednesday night due to flooding. Early on Thursday, they were advised it was not safe to return.

“We estimate up to 130 properties may be impacted,” the State Emergency Service’s David Baker told ABC TV.

“It’s mainly homes in that area, rural homes, that may see what we call above-floor inundation.”

Baker said the next few days would be challenging but further heavy rain was not expected.

“The big tap in the sky has been turned off – that’s great news for us,” he said.

“What we’re dealing with now is what’s currently in the river systems that will need to flush itself through.

“We can assess that and we can manage that and put efforts in place to make sure that communities are out of harm’s way.”

Tweet from @NSWRFS

Rain douses flames

In NSW, substantial rain has brought relief to firefighters containing a major blaze on the south coast, but it has complicated matters for other emergency crews working across the state.

At least 20 millimetres of rain overnight dampened activity across the fire ground near Bermagui and enabled crews to strengthen containment lines on Thursday, the NSW Rural Fire Service said.

Hotspots were being extinguished near Cuttagee and Barraga Bay as mopping up continued further south for the Bega Valley bushfire.

“Firefighters are back out on the ground today, making sure we’re taking care of smouldering logs and dangerous trees,” RFS spokeswoman Victoria Quested said.

While the fire is being contained and cooler conditions are expected to last several days, the RFS warned there was an increased risk of falling trees and pockets of active fire.

Strengthening winds on Thursday might also lead to some reignitions within the burnt area, it said.

At least four homes and a shed have been found destroyed. That number could increase as assessment teams completed their survey of the area.

At 6700 hectares, the fireground is now more expansive than Sydney Harbour.

The bushfire was brought under control overnight after spreading rapidly in hot, windy conditions on Tuesday.

Bega Valley residents will have access to disaster assistance under Commonwealth-state recovery funding arrangements.

NSW Emergency Services Minister Jihad Dib said the assistance would support communities, landowners, farmers and primary producers in the clean-up and recovery after the bushfires.

There were 42 grass and bush fires burning across NSW on Thursday afternoon, while high fire danger ratings were in place for the greater Sydney, Hunter, north coast, northern slopes and north-western regions.

Temperatures were expected to be close to the October averages across much of the state. But damaging winds hit the north, central and southern ranges and parts of the south coast in the morning.

Sandbagging was also being done near the Victorian border, where there was riverine flooding.

SES assistant commissioner Sean Kearns praised the public for heeding safety warnings amid wild weather, with no reports of injuries or rescues.

-with AAP