"The External Affairs Ministry has expressed its concern to the Australian Government that Dr Mohamed Haneef should be treated fairly and justly under Australian law," said a ministry spokesman.
Sources said that India was seeking consular access to Haneef irrespective of whether he continued to be held in police custody or in immigration detention at Villawood.
In Australia, a spokesman for the Foreign Affairs Minister, Alexander Downer, said all efforts were being made to keep Indian authorities informed on both criminal and immigration developments.
Australian intelligence authorities are investigating a report in the Indian newspaper The Asian Age that alleged Dr Haneef was a senior organiser for the now-banned group the Student Islamic Movement of India (SIMI), when he was at medical school.
But Haneef has denied the allegation, his solicitor says.
Meantime a 142-page transcript of a taped Australian Federal Police (AFP) interview with Haneef is doing the rounds in the media there.
Haneef reportedly told told AFP Agent Adam Simms that he had never had firearms, explosives or terrorist training and denied he had ever been asked "to take part in jihad or anything that could be considered similar to jihad."
In the interview, he insists he is a Muslim with moderate views and contends he is being "framed" over a mobile phone SIM card he gave to his second cousin.
The 27-year-old doctor describes jihad as a life struggle rather than a violent revolution.
In an interview after his arrest at Brisbane Airport on July 2 for allegedly supporting a terrorist organisation, Dr Haneef said:
"I'm clear from any of the things.
"I haven't done any of the crimes.
"And I don't want to spoil my name and my profession.
"And I've been a professionalist (sic) until now and I haven't been involved in any kind of extra activities."
He has admitted to obtaining a loan in June 2004 from Glasgow bombing suspect Kafeel Ahmed, for a medical qualifying examination.
"When I asked him (when to) pay him back, he said just give it to any of the poor in India," Haneef said.
He also transferred $A2,100 that he said was intended for his family from England to India using Kafeel in October 2005.
The AFP says it suspects Haneef may have known about the terrorist attacks in Britain before they were hatched.
Dr Haneef said that his father-in-law had booked and paid for a one-way ticket to India scheduled for July 2 "because I didn't have any money."
"I asked him to book a ticket for me now and ah, I (was) going to get a ticket...with my money when I come back."
A year earlier he had given his mobile phone SIM card, which had unused credit, to his second cousin Sabeel Ahmed.
Dr Haneef said he mentioned to his father-in-law that Ahmed had been arrested over the foiled terrorism attacks in London and Glasgow.
"So (my father-in-law) he said to me 'Why are you worried about that?' So I just said 'keep calm, if we have not done anything, then just nothing to worry'."
Dr Haneef told the AFP he was told by his father-in-law to call British police and "let them know what's going on."
Dr Haneef said that he made repeated telephone calls to police officer, Tony Webster, in Britain to explain the SIM card issue, but the calls were unanswered.
Meanwhile, AFP Commissioner Mick Keelty says the prosecution's case against Haneef has been undermined by the leaking of the transcript.
"We now have a published document that has provided information that should never have been provided until the court had an opportunity to hear it for the first time and test the veracity of that evidence," he told ABC radio.
In a related development, Immigration Minister Kevin Andrews said Haneef will remain in detention until his trial and after that it is very unlikely he would be allowed to remain in Australia.
"The Federal Police will issue what's called a criminal justice certificate," he said adding "That means he will remain in Australia while the legal proceedings are on foot," according to ABC Online news.
"After that, unless there's some new information provided or if there is some change as a result of legal proceedings, he would be deported," he said.
Meantime in Bangalore in southern India, police said Kafeel Ahmed, , who drove a blazing jeep into Glasgow airport, had a dream of constructing a housing complex on the outskirts of Bangalore where Shariat would have been the rule of law.
An analysis of his computer hard disk showed a detailed project in which Kafeel wanted to purchase a land of five acres in or around Bangalore where a housing complex could be set up, officials carrying out his background check said.
They said Kafeel's dream project showed that he wanted Shariat law to be followed in letter and spirit at the proposed housing complex.
He had been visiting several religious and secessionist sites, including Jamat-ul-Dawa, the parent organisation of militant outfit Lashkar-e-Tayiba.
Kafeel had also been attending religious meetings and opposed modernisation of Islam, the sources said.
In January this year, Kafeel had disrupted a meeting organised by a Bangalore-based organisation to discuss reform in Islam.
Security agencies were for the time being inclined to rule out Kafeel's association with any of the deadly terror groups like Al Qaeda as was evident from the bombs he tried to assemble with information gleaned from Web sites. He had little practical knowledge of explosive devices.
It is also claimed that he sent his brother Sabeel (also charged in the case) sent a text message after the car bombs were planted in London, but before the attack on Glasgow Airport. The message contained the password for an Internet email account.
Inside the email account was a folder containing Kafeel's last will and testament and instructions on what to say to the police.
The instructions told Sabeel to say Kafeel was working on a project about global warming and was on holiday in Iceland and keep saying that to anyone who asked about him.