Prime Minister Julia Gillard has ordered for a sweeping overhaul of security measures on Australia's key waterfront areas following reports from police authorities that confirmed the operations of criminal groups in Brisbane and Melbourne.

Ms Gillard's main man on the task, according to the Australian Associated Press (AAP), is Home Affairs Minister Jason Clare, who admitted earlier that "organised crime is an insidious presence in Australia ... it costs our economy over $15 billion a year."

The reinvigorated attention coming from the federal government, Mr Clare added, should disturb the rampant illegal activities that were earlier detected by local officials in Sydney.

"This is a major crackdown on organised crime and a major overhaul of security of the waterfront and the entire supply chain," Mr Clare told The Age in an interview.

He added that the fresh government initiative was prompted by the sterling achievements of police authorities in New South Wales, which had earlier established a taskforce codenamed Polaris that was deployed to neutralise organised criminal groups in Sydney's port area.

Polaris, the minister said, was credited in clamping down the inflow of illegal drugs through one of Australia's main entry point, its works resulting too in the arrest of many individuals suspected of links to organised criminal operations.

The taskforce's success has convinced the national authorities to set up similar operations in Brisbane and Melbourne waterfronts, which were also believed to have been intruded by criminal elements, Mr Clare said.

"We've seen organised criminals either targeting stevedores or getting jobs on the wharf, working inside private companies and trying to access the integrated cargo system," the federal official said in an interview with ABC.

Local authorities, Mr Clare added, have asked for federal support and the government has responded by providing police "the extra power to revoke the right of somebody to work on the dock if they've got compelling intelligence that person is involved in organised crime."

The main component of the security fixes thought by police authorities is the impending introduction of a revised maritime identification card, which will replace the old system that officials said has been compromised through corrupt dealings by some in the government service.

This early, Mr Clare has acknowledged the reality that Ms Gillard's reform quest would be met by some amount of opposition from those on ground but he vowed: "I'm not backing away from that and I think that this will be controversial."

The waterfront reforms, according to The Age, will also check on the extent of infiltration that organised crimes have so far achieved in numerous players operating in the port areas, which basing on the findings submitted by NSW officials would implicate custom brokers, cargo handlers and freight forwarders.