In a damning new revelation indicting the Australian police in the bungled Haneef case, an inquiry has been told that the federal force ignored repeated warnings of insufficient evidence against the Indian  doctor, wrongly charged with a terrorism-related offence.

In a formal submission to the John Clarke inquiry, the Queensland police service said it did not believe there was enough evidence to charge the 28-year-old Gold Coast doctor, who was forced to spend nearly three weeks in detention, and that it advised the federal police accordingly.

'In terms of charging Haneef, the QPS, based on what  was known to it at the time, provided advice to the Australian federal police that the QPS was of the view there was insufficient evidence to support a charge against Haneef,' the documents were quoted as saying by The Age daily.

The submission revealed that four or five times in the day before Haneef was charged, Queensland police officers reiterated their opinion that there was insufficient evidence.

One senior Queensland officer, detective superintendent Gayle Hogan, said she was present when the Australian federal police's senior investigating officer in Brisbane, Ramzi Jabbour, spoke to senior management by phone and advised them of the the Queensland police's opinion.

'Detective superintendent Hogan was then advised by senior investigating officer Jabbour that he was going to charge Haneef,' the submission said.

The AFP had received severe flak over its handling of the case as Haneef was kept in detention for three weeks following his arrest at Brisbane airport on July 2 last year in connection with the failed London [Images] bombing, only to be absolved later. The criticism prompted the government to launch the Clark inquiry in April.

Haneef's solicitor Rod Hodgson said the inquiry would need to determine who ultimately decided to charge his client and claimed the actions could have been politically motivated.

"If one law enforcement agency felt there was not sufficient evidence, why did another agency consider there was sufficient evidence? That raises questions that the Clarke inquiry will have to address about possible ulterior motives for the charge being laid," Hodgson said.

Queensland police provided intelligence, laboratory and investigative support for the Haneef case.