The Australian Federal Police (AFP) say their investigations will continue despite dropping a terrorism-related charge against Indian doctor Mohamed Haneef.

Dr Haneef has been in custody for almost four weeks and was charged two weeks ago with recklessly providing support to a terrorist organisation.

In the Brisbane Magistrates Court this afternoon, the AFP applied to have that charge dropped.

An application to amend the charge against Dr Haneef was adjourned this morning pending the outcome of a review of the case against him by the Commonwealth Director of Prosecutions (DPP).

The matter resumed this afternoon when senior counsel Alan McSporran announced to the court that the DPP found there was not a reasonable prospect of a conviction.

At a press conference this afternoon, the Commonwealth DPP Damian Bugg QC said the charge had been dropped because a mistake was made in the case.

"On my view of this matter a mistake has been made and I will examine that because to me the primary decision to make was to determine whether or not this prosecution was on sound footing or not, I've made that determination," he said.

"I'll now take further steps to inquire as to how that mistake occurred."

Mr Bugg says one of the significant errors in the handling of the case was about where Dr Haneef had lived in the United Kingdom.

He says the other error was that the prosecutor told the court that Dr Haneef's phone SIM card was found in a burning Jeep at Glasgow airport when it was actually found in Liverpool.

"His explanation was that he came to court in a hurry, he was provided with information and the information that he was working from was not a standard statement of facts form where everything was in precise detail," he said.

"He was also working from his recall of a range of discussions the day before and he's made an error."

Mr Bugg conceded the decision to drop the charge was upsetting.

"I'm not embarrassed about it, I'm disappointed."

On the subject of whether he would apologise to Dr Haneef, Mr Bugg said: "I'll consider that when I've completed my investigation."

Mr Bugg says it is not possible to release too many details about reasons for reaching the decision to drop the charge because investigations are still under way in the United Kingdom.

While he acknowledged that errors had been made, he says an assessment of the handling of the case should be made in context.

"It's very easy for commentators to sit back and see chinks in a process that has been undertaken in very extreme conditions," he said.

Investigation 'continuing'

AFP Commissioner Mick Keelty supports the decision to drop the charge.

"Cases are brought before the courts on a number of occasions where matters do not proceed because of one reason or another," he said.

He also defended Mr Bugg for his error.

"Advice and information is going to change in an investigation that is so broad," he said.

He says tens of thousands of exhibits had been presented in the case thus far.

Commissioner Keelty says while the charge against Dr Haneef had been dropped, the matter did not end there.

"The investigation is continuing ... we don't intend to scale down the investigation," he said.

"It's a very broad-ranging investigation."

He also defended the actions of his officers.

"The team has at all times acted professionally," he said. "The police investigation has been thorough and it will continue to be thorough."

Mr Bugg says given the difficulties inherent in investigating matters that took place on the other side of the world up to a year ago, criticism of the investigation was unfair.

He says time pressures were also a factor in the investigation.

But he says he believes he retains the confidence of Attorney-General Philip Ruddock.

"He understands from that explanation what has occurred. He knows that I have a job to do ... and I'd like to think he still has confidence in the job that I do," he said.

Visa

Dr Haneef's legal team will now concentrate on preventing his deportation after Immigration Minister Kevin Andrews cancelled his work visa.

Solicitor Peter Russo says he expects to receive material from the Immigration Department on Monday if the Government is to proceed with the deportation.

Commissioner Keelty says the information given to Mr Andrews regarding Dr Haneef's visa still stands correct.

He also says it is up to the Mr Andrews and Mr Ruddock to decide if Dr Haneef should be allowed to remain in Australia.

Dr Haneef's relative Imran Siddiqui says the family will fight to clear his name completely.

On Wednesday, Mr Bugg took the unusual step of initiating a review into the case.

Yesterday the former chairman of the National Crime Authority, Peter Faris QC, said the DPP's decision to review the case suggested the case is about to collapse.

"This is the end of the case against Mr Haneef," he said.

"I have no doubt that the reason that [Mr] Bugg has intervened is to find a way out of the impasse that the DPP finds itself in, which is, to put it bluntly, they have no case."

But Commissioner Keelty rejected any suggestion the AFP had mishandled the case.

But Queensland Council of Civil Liberties spokesman Michael Cope says there should be an inquiry into how the case has been handled.

"We call for perhaps a Senate inquiry into the handling of this matter," he said.

"There's got to be serious issues raised about this handling either by the AFP or the Director of Public Prosecutions."