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.

Australian Associated Press