As retailers prepare for Christmas sales, DP World Australia closed its Sydney, Melbourne, Brisbane and Fremantle port operations after detecting the breach on Friday, leaving cargo and containers stuck on the docks.
The federal government is helping co-ordinate the stevedore's response and the Australian Cyber Security Centre is providing technical advice.
"DP World is responsible for the movement of 40 per cent of freight in and out of our country. It is essential to the functioning of our economy," Cyber Security and Home Affairs Minister Clare O'Neil told ABC Radio on Monday.
"It does show how vulnerable we have been in this country to cyber incidents and how much better we need to work together to make sure that we keep our citizens safe."
DP World, which is Australia's biggest ports operator, expects to be up and running again within days, having cut off its internet to stop ongoing unauthorised access to its network.
That measure however also resulted in key systems linked to its port operations not functioning normally.
The former head of the Australian Cyber Security Centre, Alastair MacGibbon, who is advising DP World, said the number one priority was to get containers moving again.
"A pretty brave and smart move was taken to pull the plug, so to speak, on the internet," he told Nine's Today show on Monday.
"It's protected the organisation against potential future harm.
"But by its nature, it creates a technical problem when you cut off the internet.
"What we're dealing with here is the consequence of reducing harm, which might sound crazy to you, but it's the safest, smartest thing for all."
Mr MacGibbon, the chief strategy officer at CyberCX, said data was taken by "someone malicious or unauthorised" but would not say what the nature of the data was.
He also said DP World had been working closely with the government at the weekend and noted that emergency supplies, such as vital medical supplies and equipment, could be picked up "selectively" from the docks.Â
"So they can deal with the most critical matters but .... the vast bulk of cargo is just stuck at the moment," he said.
Australian Industry Group CEO Innes Willox said the disruption could result in shortages or flow-ons in higher prices if the issue drags on.
"The longer this goes, the more difficult the consequences will be," he told Nine.
"We think that most retailers are OK for Christmas - that's the indication we've had."