Authorities are concerned that organised criminals are using bribery and other means to try and corrupt Australia's visa system - potentially for terrorism or fraud.
It's also feared some businesses are establishing inappropriate relationships with public officials in a bid to bypass the country's strong biosecurity controls.
The head of the Australian Commission for Law Enforcement Integrity on Tuesday warned a parliamentary committee looking into Australia's border arrangements that both were significant issues.
Michael Griffin, who oversees a number of agencies including federal police and Border Force, said organised crime groups are motivated by the fact Australia is one of the world's most profitable markets for illicit drug importations.
He said there were a lot of indicators of criminals attempting to corrupt the visa issuing process both domestically and offshore to enable organised crime, possibly terrorism and commercial fraud.
"They are the traditional methods of corrupting officials through the use of influence, through extended family relationships, through bribery, through entrapment processes - we are seeing that," Mr Griffin said.
"It is of such significance to draw our attention and to have us focused very closely on it."
He also expressed concern about the possibility of unscrupulous businesses circumventing Australia's border regulations through forming corrupt or inappropriate relationships with public officials.
"It is premature for me to say much more in public, although it is enough to say that this type of corruption may introduce significant biosecurity risk through lax procedures in the screening of agricultural imports," he told the hearing in Canberra.
The watchdog has uncovered a number of cases of officials accepting "very substantial bribes".
Mr Griffin noted 26 matters had been prosecuted and convicted recently, ranging in punishments of up to 14 years in jail.
The AFP is also concerned organised crime figures are getting work at airports and ports and exploiting their security passes.
It has identified drug importations facilitated by "trusted insiders" in aviation.
"Airport criminal infiltration may exploit vulnerabilities across a lengthy supply chain from airport logistics and functions, air freight logistics, security, baggage handling and even air crew," AFP Assistant Commissioner Neil Gaughan told the inquiry.
More than 60 organisations and companies can issue aviation and maritime security identification cards, with the AFP warning the more people who can dish them out, the more vulnerable they become.
The Office of Transport Security, which regulates Australia's airports, ports and and offshore oil and gas sites, is pursuing a raft of measures to crack down on staff security.
Anyone with links to serious or organised crime would be blocked from getting identification cards under legislation before parliament.
The agency is boosting screening of airport staff working in restricted areas, expanding the scope of background checks and forcing those who issue ID cards to verify identities face-to-face.
They're also looking at the design of the aviation and maritime ID cards, including their security features.
OTS executive director Sachi Wimmer told the inquiry the agency was investigating the possibility of introducing biometrics into the cards and cutting the number of people who can issue them.