SBS Channel revealed a dossier said to be made by Bangalore police on Haneef which alleges he "must have come into contact with members of terrorist entities and assisted".
One entry in the file, which is marked "restricted", said "Organisational set up: alleged links with Al Qaeda".
But the document does not provide any evidence and it is not clear whether police were just outlining suspicions to be further investigated.
Haneef's lawyer Peter Russo is sceptical.
"My understanding is that it was just a vague reference in a document, it doesn't say how or what supports it," he said last night adding the information was not put to Haneef during interviews with Australian Federal Police.
"No, my understanding or my memory is that he wasn't directly asked," he said. "I know he was questioned about his education, where he went to school and what type of school he went to, etc."
AFP Commissioner Mick Keelty today said the alleged links were new information to him.
"We don't have anything that positively says that in Australia but of course it is an avenue of inquiry and if that is what the Indians are saying it needs to be followed through," he told ABC radio.
The dossier also said Australian police found a bank locker key on Haneef, which did not belong to him, according to ABC report.
Keelty said the AFP were probing a "money trail" in the ongoing probe into claims Haneef had links to al-Qaeda.
"Some of those avenues of inquiry I can confirm relate to financial transactions, but as I keep saying this is very much an ongoing investigation, it's a live investigation, and we need to let the investigation take its course."
Asked if investigators were following a "money trail", Keelty said, "We are."
Keelty said Australian authorities had no evidence that Haneef was linked to al-Qaeda, but the allegations need to be followed up.
Australian Health Minister Tony Abbott said there is no reason to believe Australian authorities knew about the Indian police file.
"I honestly don't know if anyone else in our security apparatus might have been aware of it, but certainly it's the kind of thing the AFP will be talking to their Indian counterparts about," Abbott was quoted by a media channel.
"I certainly didn't know about it, it's not in my portfolio area, but I have no reason to think anyone else would have known about it" he said and added there were advanced plans to have a system of national medical registration, which would mean a high uniform Australian standard for foreign trained doctors.
"The vetting process is as reasonable as we can make it but it is not absolutely foolproof and we're trying to make it better," he said.
27-year old Haneef, whose work visa was cancelled by Andrews on character grounds, was released from custody Friday last after terror charges against him in connection with the failed car bombings in the UK were dropped due to lack of evidence. He returned to India at the weekend.