An intense storm system that has dumped “mind-boggling” rain over parts of Victoria is expected to unleash into Thursday, as NSW also faces severe weather.

The latest emergency flood warning in Victoria was for the Macalister River in Gippsland, which was already at major flood level on Wednesday afternoon.

The Bureau of Meteorology has issued storm warnings for eastern Victoria, southern NSW and the ACT on Wednesday and into Thursday.

The most serious was for Canberra, where the weather bureau warned “severe thunderstorms with damaging winds [were] likely” on Wednesday afternoon.

Tornadoes haven’t been ruled out in southern NSW as the system brings damaging winds and heavy downpours.

The wet change has been welcomed by firefighters battling blazes on the NSW south coast and Victoria’s east Gippsland region.

Three homes were lost on the NSW south coast at Coolagolite on Tuesday night.

Crews got some relief when a cool southerly change moved across the fireground early on Wednesday. But it brought the next threat, with communities in both states facing the threat of flooding.

There are several other flood warnings across eastern Victoria and the NSW south coast, including places hit by bushfires on Tuesday and Wednesday.

Areas in NSW that may be affected by flooding include Nowra, Eden, Bega, Katoomba, Cooma, Albury and Hay.

For Victoria, there are heavy rain and strong wind warnings for east Gippsland and parts of north east, west and south Gippsland.

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Flooding may occur at Corryong, Bright, Orbost, Falls Creek, Mount Hotham and Omeo.

Parts of Victoria on Wednesday have been slammed with record-breaking rainfall in the past 24 hours.

Forecaster Weatherzone said “mind-boggling” rain fell at Mount Hotham, in the Victorian Alps, which had 198.8 millimetres to 9am Wednesday – its wettest day in any month in at least 46 years of records.

There were also heavy falls of more than 100 millimetres west of the mountains across large low-lying parts of northern and central Victoria.

Lake Eildon, which sits in low hilly country east of Mount Buller, had its heaviest October day of rainfall in 135 years of records, with 106 millimetres.

Shepparton had 67 millimetres in the 24 hours to 9am, almost as much as it received in the whole of winter 2023, according to Weatherzone.

“Rain will increase in much of eastern Victoria throughout Wednesday, with winds having swung to the south in the wake of the cold front. Light snow is also already falling in parts of the Vic Alps,” the forecaster said.

“Rain will also persist in north-east Victoria and large parts of NSW as the relatively slow-moving cold front and associated rainband tracks east.

“Storms could be a feature of the weather in NSW on Wednesday afternoon, and the BoM has even mentioned that tornadoes cannot entirely be ruled out.”

Weather conditions are expected to ease from Thursday but flooding is tipped to last until the weekend.

Watch and act alerts for flooding were issued on Wednesday across eastern Victoria for as far north as the King River at Cheshunt down south to Glenmaggie.

Residents along the Acheron River near Marysville and the Goulburn River near Lake Eildon were warned moderate flooding was expected after 140 millimetres of rain in the 24 hours to 5am.

An alert was also issued for parts of the Yarra River on the outskirts of Melbourne.

Victoria had hundreds of calls for help as rivers continued to rise.

Emergency Services Minister Jaclyn Symes said there were more than 300 requests for assistance to the State Emergency Service overnight, mostly connected to flooding near Eildon.

The flood threat comes after many residents in Gippsland were put on alert for fires.

About 700 firefighters spent three days battling two separate blazes, with one home lost in Briagolong but no reports of serious injuries.

The cause of that blaze, which grew to about 17,500 hectares, is under investigation.

Days to assess south coast damage

Meanwhile, it will take days to fully assess the damage to homes and property after a bushfire ripped through dense bush on the NSW south coast.

The NSW Rural Fire Service has confirmed the loss of properties in the Coolagolite fire, but officials were unable to send building assessment crews onto the 5200-hectare fireground until Wednesday afternoon.

Work to contain the blaze, south-west of the coastal town of Bermagui, and remove hazards was ongoing, the RFS said.

“We certainly wouldn’t want the [assessment] crews on the ground and having trees falling, for example,” spokeswoman Victoria Quested said.

“It’s not just a matter of putting the fire out.”

The blaze continues to burn near homes in the Cuttagee, Barragga Bay, Murrah, Bunga and Goalen Head areas after torching an area the size of Sydney Harbour inside 24 hours.

There have been no reports of missing people.

Evacuated residents, including about 65 people put up in caravan parks and motels, were asked to steer clear of the area until it was safe, Bega Valley mayor Russell Fitzpatrick said.

Premier Chris Minns said firefighting crews had been through a tough 24 hours as they worked to protect towns, many of which were full of holidaymakers for the school holidays.

“We’re in October and we’ve found that we’re facing midsummer bushfire conditions in some parts of NSW – it points to a hellish three months,” he said.

Warmer conditions on Thursday were expected to return the fire danger to high for the south coast before risks eased again at the weekend.

“There is reprieve on the horizon in terms of the weather, but we’re not necessarily out of the woods yet,” Quested said.

Conditions also improved in many other parts of NSW as crews battled 63 bush and grass fires.

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-with AAP