It follows an investigation by the Global Mail which quoted Pakistani officials confirming that Australian Federal Police had encouraged a policy of racially profiling people from the Hazara community, suspected of preparing to flee the country.
Hazaras are Shia Muslims and often face persecution from Sunni death squads in Pakistan. Their distinctive East Asian facial features make them an easy target.
"In getting involved with the intelligence agencies in Pakistan, Australia is involving itself in a very sordid and questionable environment, in which these Hazaras are facing really shocking threats, and are literally being killed every week," Mustafa Qadri, a Pakistan researcher with Amnesty International, told Radio Australia.
Mr Qadri said it was known that Australia was providing financial and other assistance to Pakistani intelligence agencies to stop a range of racketeering in the country, including people smuggling.
"The Australian authorities are trying to disrupt the smuggling but in the process effectively supporting elements involved in a range of very sordid things," he said.
"What we also see on the ground is that Australian authorities are trying to stop people from coming to Australia by saying that they won't get asylum in Australia, that it's on a very arduous journey ... this is PR against that."