Operations at its container terminals in Melbourne, Sydney, Brisbane and Perth have been suspended since Friday.
DP World Australia manages around 40% of goods entering and leaving the country.
The move has not affected the supply of goods to major Australian supermarkets, the BBC understands.
DP World Australia, a unit of the Dubai state-owned DP World, did not immediately respond to a request for comment on Monday.
Darren Goldie, the government's Cyber Security Coordinator, said the operator was making "good progress" at bringing its sites back online.
"The company's advice... was that this would be the case of days, not weeks," Mr Goldie told ABC Radio.
He added that the government had not yet identified the perpetrators of the cyber-attack, which caused the firm to disconnect its ports from the internet.
DP World said it halted internet connectivity at its ports on Friday to prevent "any ongoing unauthorised access" to its network.
Going offline meant trucks were unable to transport containers in and out of the affected sites. That's according to DP World senior director Blake Tierney in statement issued on Sunday.
On Monday, Ports Australia, which represents authorities and companies in the industry, said "The current disruption is isolated to DP World terminals."
"Australia's ports and other terminals remain operational. DP World is collaborating closely with the government and working to restore normal operations," it added.
Double whammy
DP World has also been affected by industrial action, which has caused a delay in customer deliveries.
Since it began in October, workers have engaged in 24-hour strikes and refused to unload trucks.
The Maritime Union of Australia, which is negotiating pay increases for workers, announced last week that the industrial action would be extended to 20 November.
The cyber-attack added to fears that the supply of everything from medical equipment to Christmas toys could be disrupted.
However, a spokesperson from supermarket chain Woolworths said it was monitoring the situation and does not "anticipate any immediate impacts at this time".
The BBC understands that Woolworths' range of Christmas products has already arrived in Australia.
The disruption is also not expected to affect rival chain Coles, which is similarly monitoring developments at DP World.
Australia has seen a rise in cyber attacks since late-2022.
Earlier this year, the Albanese government announced plans to overhaul its cybersecurity laws, and set up an agency to coordinate responses to intrusions.
The government is expected to released details on its proposed rules next week - which will likely tighten reporting requirements for companies.
By Annabelle Liang
Business reporter