The fire broke out late on Wednesday at the Viva Energy Geelong refinery, southwest of Melbourne, which supplies more than half of Victoria's fuel and about 10 per cent nationwide.
Prime Minister Anthony Albanese is visiting the site on Friday morning after flying home early from a trade mission to Malaysia, describing the scenes of the blaze as "very distressing".
The refinery, which has been operating at full capacity in recent weeks, will be slowing its output for the time being, Viva said.
On Friday, Deputy Prime Minister Richard Marles described the incident as significant but deferred to the company's assessments on supply impacts.
"They are hopeful that this will have a relatively minimal impact on supply," Mr Marles told ABC from Geelong.
"It was a significant incident, and I should say that, you know, we are deeply thankful that no one was hurt or injured."
The fire alone, suspected to have been caused by a gas leak, will be unlikely to bring Australia closer to stage three of its four-stage national fuel security plan, he said.
"Obviously the timing of this is terrible, so there's no getting away from from that," Mr Marles said.
"I don't think what's happened here moves us from one stage to the other, but obviously that's a set of circumstances that we continue to monitor."
Australia is currently at stage two of the national fuel security plan, a practical guide aimed at managing supply challenges related to conflict in the Middle East.
Exactly what the next stage, stage three, would look like is not clear, but would involve practical measures to limit fuel use.
The fire primarily affected infrastructure responsible for the production of petrol and aviation gasoline, which is distinct from jet fuel and usually used by small aircraft.
Production of diesel and jet fuel is continuing at the site at temporarily reduced levels as a safety precaution, the company said.
Fortunately, petrol has been least affected by supply headwinds related to Iran's effective closure of the Strait of Hormuz, Mr Marles said.
"Diesel and jet fuel, which are more under pressure, would not be affected in terms of the refining capability here," he said.
Mr Albanese cut short his visit to Malaysia on Thursday night to visit the refinery along with Mr Bowen and Mr Marles.
He described images of the fire as "very distressing" and said assessments would be carried out to determine the fallout.
"Clearly there will be consequences for it, but there'll be a proper assessment taking place over the coming short period," the prime minister said.
"We'll continue to work with the company to do what we can to make sure that anything that is offline is brought online as soon as possible."
On Thursday, Energy Minister Chris Bowen said the company was confident it could replace any production shortfall caused by the blaze with imported fuel.
"Viva is confident that they will be able to replace the impacted petrol production with imports," Mr Bowen told reporters.
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