The murky behind-the-scenes battle to discredit the AFL and the Australian Sports Anti-Doping Authority continues, with a leaked affidavit of an AFL investigator suggesting there was a "joint investigation" with the anti-doping body.

The affidavit by Brett Clothier, the AFL's integrity services boss, was lodged in September. It is Clothier's response to the case brought against the AFL by Essendon doctor Bruce Reid in the Supreme Court last year.

While Clothier states it was a joint investigation in the document filed through Minter Ellison lawyers, he also admits in the same paragraph that he "regularly shared updates and information with the ASADA investigators", a point allowed under ASADA's code.

The Bombers and suspended coach James Hird are alleging the investigation into the club's 2011-12 supplements program was unlawful as ASADA, an independent body, worked outside its legislative scope.

ASADA has denied this during the initial directions hearings in the Federal Court, and is said to have elaborated on this in its defence documents, which were lodged with the Federal Court on Thursday evening.

Reid was initially one of four Bombers charged by the AFL for governance failures, but he launched legal action. The AFL dropped all charges against him weeks later.

On his role in the investigation, Clothier wrote: "In my role as Manager - Integrity Services, I was charged with the responsibility to undertake an investigation into production, distribution, purchase and use of prohibited substances in the AFL. In part this has involved an investigation into the alleged Essendon Football Club supplement program in 2011 and 2012. I was delegated this responsibility pursuant to a delegation from the then acting general manager football operations, Mr McLachlan.

"As a result of this delegation, I was in full charge of the conduct of the investigation and not subject to direction by any other person as to the manner in which the investigation proceeded.

"The investigation was a joint investigation conducted with the Australian Sports Anti-Doping Authority. Throughout the investigation I regularly shared updates and information with the ASADA investigators."

Clothier also revealed Deloitte had been contracted to analyse the documents secured from the club, while an AFL intelligence analyst, Chris Wittock, dissected the league's database of documents and reported his findings to Clothier. Clothier did not participate in the interviews with players and officials.

Interestingly, Clothier says he did not provide updates of the investigation to former AFL chief Andrew Demetriou. Instead, he updated Gillon McLachlan, now AFL boss, AFL general counsel Andrew Dillon, AFL manager of legal and business affairs Simon Clarke and Peter Harcourt, the AFL's medical director.

Clothier says he agreed with ASADA that it would provide an interim report. This report is being used as a way for Hird and the Bombers to suggest there had been an "improper purpose" to the investigation, that being it was also about possible governance failures as opposed to ASADA's anti-doping brief.

The affidavit also provides official background on the handling of one of the peptides initially at the centre of the investigation, the anti-obesity drug, AOD-9604. This came when Dr Andrew Garnham, who had previously sat on the league's anti-doping or illicit drug code tribunal, was given permission to be a consultant for the Bombers.

Six days after Essendon self-reported on February 5 last year, Garnham, in an email to Harcourt, said he thought AOD-9604 was banned under WADA's S2 (not prohibited) and catch-all SO (non-approved) clauses.

Harcourt, however, replied that it was "undetermined", while ASADA's Dr Stephen Watt said he had "clear advice from WADA that it is not prohibited under S2 but it appears that the SO question has not been addressed". That it took until April last year for WADA to clear up the issue and declare AOD-9604 fell under SO meant ASADA could not use it as part of its case.

The 34 current and former players issued with show-cause notices are alleged to have been administered the banned Thymosin beta 4.

The AFL did not wish to comment when contacted on Friday.