Corruption investigators charged Order of Australia recipient Anthony Dieni, who works at St Paul's Prevention Rehabilitation centre, on Tuesday morning.

Allegations against Mr Dieni, 69, of Keilor Lodge, include stealing $164,000 from his clinic, accepting drugs as payment and providing a urine sample from a third person in a drug test of one of his patients.

Mr Dieni faced the Melbourne Magistrates Court on Tuesday afternoon on charges of trafficking a drug of dependence, perverting the course of justice, perjury, and theft and dealing in the proceeds of crime.

The charges follow an investigation by Victoria's Independent Broad-based Anti-corruption commission, into allegations the rehabilitation centre, a registered charity in Strathmore, has been providing false information to support bail applications and help reduce sentences.

IBAC investigator Emily Scott told the court Mr Dieni, the centre's sole counsellor, was not a medical practitioner and did not hold other official qualifications.

"He does not appear to engage in any legitimate counselling at all," she said.

Ms Scott said 10 of Mr Dieni's patients formed part of IBAC's investigation.

One patient, Patricia Martin, avoided jail in July after Mr Dieni provided allegedly false evidence she had attended the clinic and was drug free.

It is alleged he provided the another person's urine sample on her behalf.

He is also accused of taking cocaine and cannabis from Ms Martin in place of fees and passing it on to his adult grandson.

Mr Dieni is also accused of stealing more than $164,000 from the clinic for personal expenses and overseas travel for his wife.

Ms Scott said two loaded handguns were found in his bedroom as well as small quantities of cocaine and ice were found in his office during Tuesday's raid.

Magistrate Ross Maxted called the charges of perverting the course of justice and perjury "serious allegations ??? that strike very hard into the administration of justice".

In 1997 Mr Dieni was awarded the Medal of the Order of Australia for "service to the community".

In 2005, Mr Dieni successfully lobbied the Howard government not to deport Mr Madafferi, who was later convicted over what was then the world's biggest ecstasy importation.

In 2008 Mr Dieni told Fairfax Media he was approached by members of Frank Madafferi's family to urge the Immigration Department to release him into his care.

"Everybody deserves a second chance," he said.

Mr Dieni also said he didn't have any idea who gangland lawyer Mario Condello - shot dead in February 2006 - was when he asked if he could volunteer as a drug counsellor in 2005.

In April 2012 Mr Dieni told a Melbourne court he'd hired another man, Richard Michail - the sergeant-at-arms of the Finks bikie gang - as a volunteer helper.

Michail was in court on theft charges after walking into a luxury car dealership in Port Melbourne, assaulting a member of staff and driving off in a $500,000 Lamborghini.

Mr Dieni reportedly said Mr Michail, who he'd hired in a "protectionist role" to help with violent addicts, had been a cocaine user but had "changed his life around."

"He was respectful," Mr Dieni said. "He had a manner about him clients just liked. He's just a likeable person."

The Age is in no way suggesting that there was any impropriety on Mr Dieni's part in the case of Mr Condello, Mr Madafferi or Mr Michail.

Mr Maxted will make a decision on Mr Dieni's bail on Wednesday.