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.
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 petrol production was underway at the refinery, along with 80 per cent of diesel production and 80 per cent for aviation fuel.
"We hope, of course, as does the company, that that ramps up over the coming period as well," Mr Albanese told reporters.
"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."
The refinery, which has been operating at full capacity in recent weeks, will be slowing its output for the time being, Viva said.
Chief executive Scott Wyatt said there was still a way to go before the site got back to previous levels.
"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."
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 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, Defence Minister Richard Marles 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.
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