Parts of Melbourne have been pelted with golf-ball sized hailstones after thunderstorms rapidly moved across much of southern Victoria, bringing damaging winds and heavy rainfall, leading to flash flooding.

Key points: Thunderstorms brought damaging hail but also much needed humidity and rain

Thunderstorms brought damaging hail but also much needed humidity and rain Fires on French Island and near Mount Buffalo remain out of control

Fires on French Island and near Mount Buffalo remain out of control For the latest emergency information, visit the Vic Emergency website

Hailstones up to 5cm in diameter were reported in eastern suburb Glen Iris, while fire-affected catchments in north-eastern Victoria and East Gippsland are now on flood watch.

While the thunderstorms have brought much-needed humidity and rain into fire-affected areas, there are fears strong winds could topple trees, create landslides and send debris onto roads.

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Victorian emergency authorities said the rainfall caused flash flooding across parts of Victoria and caused significant damage in Melbourne.

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Victorian SES commander Jackson Bell said crews were assessing the damage.

"We've got a number of units out assisting the community to clear a lot of that debris, some of the debris includes things like smashed skylights from rather large hail the size of cricket balls, and it's caused quite a number of damages," he said.

Golf-ball sized hail hit parts of Melbourne on Sunday afternoon. ( Supplied )

Earlier, a Bureau of Meteorology forecaster said Victoria was "about to see its wettest two-day period in many, many months".

Showers and storms have already hit Wangaratta, Shepparton, Healesville, and Warragul.

That's the wrong kind of cricket ball! Ruby Cullinan, 14, (left) and Minnie O'Sullivan, 14 (right) at the Burwood Cricket Club. ( Supplied: Cathy Jacobs )

A severe thunderstorm warning remains current for damaging winds and heavy rainfall for all of Gippsland, and parts of the northern country.

A separate severe thunderstorm warning for Melbourne has been cancelled.

Hail pictured in the eastern Melbourne suburb of Camberwell. ( Twitter: @GeeForce77 )

Flash flooding of up to 50mm was likely to affect Shepparton, Seymour, Wangaratta, Traralgon, Moe and Bairnsdale.

Vast amounts of vegetation burnt over the past month have created the potential for flash flooding to sweep debris into waterways and onto roads and cause landslides.

While there is the potential for dry lightning to strike, the high humidity will likely suppress any new fires from flaring.

Hailstones as large as golf balls fell in Caulfield South. ( Twitter: @emmaatkinson )

The focus will swing to central, eastern and southern Victoria.

$75m put towards official clean-up

State Emergency Services Minister Lisa Neville announced on Sunday that the state and federal government had come together to jointly provide $75 million for Victoria's clean-up program.

The program will demolish, remove and dispose of all buildings destroyed or damaged beyond repair.

Insured and uninsured property owners will not be required to contribute to the cost.

The State Government appointed Grocon as the contractor and said the clean-up would begin within weeks.

Flash flooding during a storm last week created a sinkhole in Keilor East. ( Facebook: Victoria State Emergency Service )

Ms Neville said the company had a good track record after it was involved in the clean-up after the Black Saturday and Wye Rive fires.

"They will employ local contractors to rebuild to put money back into the community," Ms Neville said.

Businesses could begin registering on the Grocon website.

Ms Neville said 396 residential properties and 614 outbuildings and sheds had been lost in the fires so far, with one community left to assess.

About 70 people wanting to return to their homes in Mallacoota will fly into the area.

The clean-up effort will help people like Cudgewa resident Joshua Collings remove what is left of his house so he can start to rebuild. ( ABC News: Matthew Doran )

Those wanting to retrieve their vehicles and campervans will be able to fly in later in the week and drive out, subject to weather conditions.

Cause of French Island fire remains unknown

State response controller Alistair Drayton said a fire that started about 4:00pm on Saturday on French Island remained out of control after being downgraded from an emergency warning to an advice warning on Sunday morning.

Ms Neville said the cause of the fire remained unknown.

The fire burnt about 85 hectares overnight and fire crews will continue to monitor the blaze.

Mr Drayton said a shed had been destroyed by fire, but he was not aware of any homes that had been impacted and had not had any reports about koala losses.

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A local business owner commended firefighting aircraft brought in to fight the French Island blaze, and said without them, the fire could have been a catastrophe for the isolated community.

Co-owner of French Island's general store and cafe, Brent Le Serve, told the ABC there had not been a "proper fire" on the island for decades.

"There's a lot of fuel out there," he said.

Mr Le Serve attributed the quick halt of the fire to the aircraft, with low tides delaying fire trucks from getting onto the island for several hours.

"The chopper and planes were the difference between absolute catastrophe and what happened," he said.

French Island General Store staff and family have been preparing 100 sandwiches for CFA crews working on the island. ( ABC News: Zalika Rizmal )

"Without them, it would have been a lot worse."

Mr Le Serve said this time of year was high season for his business.

"On any given day, we might have 100 people coming into the store," he said.

Mr Le Serve helped evacuate about 15 people to the Tankerton Jetty on Saturday afternoon.

The evacuees included about 10 people who had rented bikes from his business for the day, and others who had planned to camp in the National Park.

'Don't treat us like outcasts'

A number of watch and act warnings remain in place for the Upper Murray and in and around Mount Buffalo and Bright.

Bruce McCallum has lived in Nug Nug for a decade and said he, his 21-year-old son, three dogs, two cats and a cockatoo had been evacuated three times in the past week and were "exhausted".

The fire came within a kilometre of the family's home and started a spot fire on one of their paddocks. It was quickly put out by their neighbours when their own fire pump failed to work.

Fires near Nug Nug and Mount Buffalo are still threatening homes. ( Supplied: Andrea Butterfield )

"There are black leaves falling everywhere, it's very calm at the moment but you can feel the sun starting to come through and it's very smoky."

Thunderstorms were predicted to come through the area on Saturday but they died out before reaching Nug Nug.

The McCallum family have units they rent out over the holiday season that were booked out for January before the fires hit the area.

"They have all cancelled. I'm also a contract engineer and haven't been able to finish any of the jobs," he said.

Mr McCallum said thousands of dollars of income had "disappeared" and encouraged Victorians to come back to the area once the fires were over.

"Don't treat us as outcasts when it's over. Make sure you can back and visit us."