The fire broke out late on Wednesday at Viva Energy's Geelong refinery, southwest of Melbourne, which supplies more than half of Victoria's fuel and about 10 per cent nationwide.
Anthony Albanese, who toured the facility on Friday morning after cutting short a trip to Southeast Asia, said the incident was regrettable, but was hopeful of production increasing again.
As of Friday, 60 per cent of the refinery's total petrol production capacity was underway, along with 80 per cent of diesel production and 80 per cent for aviation fuel.
Mr Albanese said the incident would not lead to fuel security measures being bumped up to level three, which would have led to an increase in voluntary measures to limit fuel use.
"The good news is ... that no one was injured in this incident that occurred, and that is a tribute to the professionalism and to the management issues that have been put in place to deal with an incident like this," Mr Albanese told reporters.
"We'll give an update tomorrow about fuel supplies that are on hand. Fuel is continuing to come in."
Australia is 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 more practical measures to limit fuel use.
The refinery, which has been operating at full capacity in recent weeks, will be slowing its output for the time being, Viva Energy said.
Chief executive Scott Wyatt said there was still a way to go before the site got back to previous levels of output.
"Any shortfalls of production, we're very confident that we can cover that with our our import program which is quite substantial," he said.
"It's been, obviously, a challenging event for our team. It's a shocking incident."
Despite the impact on production, he said costs would not be passed on to drivers.
"Whatever costs this incident has caused the refinery will be absorbed in our refinery operations," he said.
"We will not be passing that on to the community."
A significant amount of maintenance had been carried out at the refinery, Mr Wyatt said.
As the prime minister visited the site, a handful of orange-clad workers could be seen arriving at the facility's main office.
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.
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