More than 1500 people have already been rescued from the coastal town by defence force helicopters and boats after it was cut off by bushfires on New Year's Eve.

"We had something like 400-plus people out of Mallacoota yesterday. We had a plan to airlift another 300 out today. Sadly smoke means that is not possible," Premier Daniel Andrews said on Monday.

"Whilst the smoke is good for fire in terms of keeping some of the temperatures down, it makes access by the air much more challenging."

Those stranded in Mallacoota have been offered a place on HMAS Choules, which has returned to the town with supplies and equipment.

It is unclear when flights can resume.

Four people missing on Sunday have now been accounted for, the premier confirmed.

He also announced a new permanent government agency, Bushfire Recovery Victoria, to be headed by former police chief commissioner Ken Lay.

It will respond to the fires, with an initial $50 million in funding.

"This is not a time-limited or an authority that's about clean-up and recovery just for these bushfires," Mr Andrews said.

"Because we're going to see longer fire seasons and we're going to see ... more and more fires, more and more damage as each fire season comes."

About 200 homes have been lost, with the number expected to rise to 300 once smoke clears and aerial assessments can be carried out, the premier confirmed.

Emergency Services Minister Lisa Neville lifted evacuation orders for East Gippsland and the northeast, allowing some 67,000 people who have left their homes a "short reprieve".

"But please be aware, very aware, that it is very likely that later this week that such an order will be issued again, depending on the forecast," she said.

"At this stage Thursday, Friday do look like fire spike days. If necessary, I will reissue that order.

"But I'm very aware that there are some communities which weren't impacted over the weekend and where people want to get back to their own homes, their own beds. That's why we've lifted this order."

There are 27 fires still burning across Victoria. All emergency warnings have been downgraded, but a total of 15 watch and act warnings remain in place.

The fires have killed Buchan man Mick Roberts and Maramingo Creek man Fred Becker and burnt through 1.2 million hectares.

Victoria Police are also investigating whether a man killed in a car crash on the Goulburn Valley Highway northeast of Melbourne last Friday will be counted as the third bushfires fatality.

Rain has started to fall, but not across all fire-affected areas and not enough to douse the fires.

"There's been a little bit of rain, but it's not making an impact on the fire. We know it won't, it will take a significant amount of rain over a significant amount of time to occur," Emergency Services Commissioner Andrew Crisp said.

He said firefighters were planning to take advantage of mild conditions to strengthen containment lines before the state warms up again later this week.

Thick smoke blanketing Melbourne and regional Victoria, meanwhile, is likely to linger for days.

Authorities advised people with lung or heart conditions, the young and old, and pregnant women to stay indoors.

Healthy people may also experience symptoms including eye, nose and throat irritation, coughing, sneezing and congestion.

UPDATE, 6.45pm: We break down the destruction of the Victorian bushfires.

EARLIER: All people missing in Victoria's deadly bushfires have been found safe, but at least 200 homes have been destroyed.

Premier Daniel Andrews on Monday confirmed the four people missing on Sunday were accounted for and no one was listed as missing in the fires that have razed East Gippsland and the northeast.

He also announced a new and permanent $50 million government agency Bushfire Recovery Victoria, to be headed by former police chief commissioner Ken Lay to respond to the fires.

"It will coordinate all government effort," he told reporters in Melbourne.

"Unlike the authority that was established in the wake of the February 2009 fires, this is not a time-limited or an authority that's about clean-up and recovery just for these bushfires.

"Because we're going to see longer fire seasons and we are going to see - we should just be honest about the fact - we're going to see more and more fires, more and more damage as each fire season comes."

Thick smoke from bushfires is likely to blanket Melbourne for days, prompting a warning from authorities.

The air quality is at its worst in East Gippsland, where dozens of bushfires continue to burn on Monday.

The Environment Protection Authority has also recorded "very poor" air quality in Melbourne's metropolitan area, attributing the smoke to bushfires burning in the state as well as in NSW and Tasmania.

Chief environmental scientist Andrea Henwood urged people to take precautions, saying the smoke will linger until Wednesday.

"Close everything up. Seal the doors. Now would be a good time to do that because this is going to persist for the rest of the day," Dr Henwood told reporters.

Chief Health Officer Brett Sutton advised people with lung or heart conditions, the young and old, and pregnant women to stay indoors.

He said healthy people may also experience symptoms including eye, nose and throat irritation, coughing, sneezing and congestion.

There are 31 fires burning across Victoria as of Monday morning, with 18 in eastern Gippsland and six in the northeast.

One million hectares has been burnt across Victoria.

Rain has started to fall, but not across all fire-affected areas and not enough to douse the fires, and is creating new difficulties.

A Forest Fire Management vehicle flipped on a greasy road on Sunday because rain had not fallen in the area for so long, Mr Andrews said.

No one in the vehicle was seriously injured.

The deadly fires have killed Buchan man Mick Roberts and Maramingo Creek man Fred Becker.

The cooler weather has allowed military helicopters to deliver supplies to isolated communities and help with evacuations, reaching 13 communities on Sunday.

They also rescued 406 people from Mallacoota but attempts to fly out another 300 on Monday were stalled because of the smoke. Navy ships brought out more than 1100 people on Saturday.

More than 3500 properties remain without power, with AusNet bringing in generators when possible and restoring the network when it is safe to do so.

All warnings now sit at a watch and act level.

The state government has announced a fund to support Victorian bushfire survivors, contributing $2 million.