The federal opposition lost its battle on Wednesday to split the bill into two, which Labor said was needed in order to do more work on the clearance process for foreign workers in maritime ports.

Labor senators argued an incident involving two Vietnamese sailors abandoning ship in Geelong showed there were still flaws in the system.

"These maritime crew visas are critical to be upgraded and reviewed," Labor senator Tony Sheldon said.

Government minister Linda Reynolds confirmed the two men were still at large, having taken their passports from the ship master's cabin.

Their visas had been cancelled and "investigations remain ongoing", she said.

Home Affairs Minister Karen Andrews said the legislation had been through three parliaments and it was about time it passed.

"Quite frankly it is beyond belief that anyone would think it is OK for people who have criminal records or criminal associates should be able to work air-side or on our wharves," she said.

Labor secured an amendment to ensure the laws are reviewed after two years and a report is published following the review.

The lower house agreed to the amendment on Wednesday evening.

Drug and law enforcement inquiries six years ago recommended Australia's airports and seaports be hardened against the risk of serious crime by strengthening identification card schemes.

Arguing against splitting the bill, Attorney-General Michaelia Cash told parliament that of the 227 card holders of concern to authorities, 73 per cent were in the maritime sector.

At present, background checks only determine whether a person may be a threat to aviation or maritime security.

They do not consider whether the person has a history of involvement in serious crime.

Qantas said the laws would strengthen existing checks and balances to prevent "privileged security access at airports being abused by criminal elements".

"We have worked with law enforcement over many years to protect against and detect criminal activity," the airline said.

"These amendments improve our ability to keep doing that. The Qantas Group will work closely with the federal government to implement these changes once they become law."

Australian Associated Press