Concerns about the legality of the joint investigation by the AFL and the Australian Sports Anti-Doping Authority were raised within weeks of Essendon self-reporting by a lawyer who previously had taken on the AFL during the Melbourne tanking investigation.

As part of the submission lodged by James Hird and Essendon in the Federal Court on Friday, detailing what the two parties will argue in their case against ASADA, it has emerged lawyer Chris Pollard was one of the first to raise concerns about the joint probe into the Bombers' supplements program.

Pollard, representing several Essendon personnel, wrote to AFL integrity officer Abraham Haddad on March 1, stating: "The code neither contemplates a 'joint' investigation nor the use of information obtained by ASADA being used by the AFL for any other purpose, save the procedures authorised under the code".

According to Hird's lawyers, the AFL responded with a "significant" admission. The AFL said it would be "playing and (sic) active role in the investigation and using all such information obtained in determining if there has been any breach of the AFL player rules and/or the code."

Pollard also raised this issue in a meeting with the AFL's integrity chief Brett Clothier, who "dismissed this opinion".

A former lawyer for the AFL Coaches Association, Pollard had represented former Melbourne coach, the late Dean Bailey, in his fight to clear his name amid the Demons' tanking debate.

Another lawyer representing Essendon staff, Ragu Appudurai, and a player interviewed at the AFL Players Association headquarters would follow Pollard's lead and also raise concerns about the probe's legality.

These arguments are set to be mentioned in the trial before Justice John Middleton, beginning on Monday.

Hird and the Bombers argue ASADA, an independent body, worked outside of its legislation, and the interim report it produced with the AFL was for ulterior purposes other than anti-doping breaches. Hird and the Bombers would later be charged for governance breaches by the AFL.

Their submission also confirms the first step in the investigation after the Bombers self-reported on February 5 last year was the acquisition of records from Geelong, Gold Coast and Melbourne. Former Essendon sports scientist Stephen Dank had had dealings with the Suns and Demons, while fitness boss Dean Robinson, the latter having been stood down on February 5, had worked with the Cats and Suns.

"The clubs other than EFC were relevant because the persons involved in the EFC supplement program in 2012, Messrs Stephen Dank and Dean Robinson (one or both) had worked at all three clubs," the submission said.

AFL chief Gillon McLachlan said on Saturday many points made by Hird and Essendon, including what he and former league boss Andrew Demetriou were told in a briefing with the Australian Crime Commission, were "mostly distraction and noise".

"There is a lot of stuff that is not relevant to next week (court case). I just want to get this resolved so we can look towards 2015," he said.

In its submission, ASADA argues that Hird did not have an issue with the joint investigation, and even "facilitated and actively co-operated with the investigation by ASADA and the AFL".

"When the question of interviews arose in the early days of the investigation, it appears that Mr Hird was keen for his interview to come on quickly. Essendon also proactively engaged with the AFL and ASADA regarding the arrangements for the interviews," ASADA argues.

While Hird maintains he was not given the right to silence under anti-doping legislation during his April 16 interview, having been compelled to tell the truth under AFL law, his lawyers wrote to ASADA and the AFL on April 15 last year and said: "Consistent with his desire to assist and fully co-operate with the on-going investigations, and not withstanding the issue of confidentiality discussed below, our client will answer all questions put to him during the interview."

Former ASADA chief Aurora Andruska also notes that then-Essendon chairman David Evans was "impressed" with how the anti-doping body had conducted itself and praised its work in February, April and June.

ASADA says had Hird and Essendon complained about any legality issues earlier, it could have gathered the same information "lawfully". For instance, ASADA could have asked the AFL to conduct the interviews without ASADA officials being present.

ASADA also alleges that "in September, 2013 Essendon was commercially leveraging off its public stance of co-operation with ASADA and the AFL in its promotional material to sponsors". By that stage, the interim report – which had caused internal divisions at ASADA and in its relationship with the AFL – had been published and punishment handed out.

Players are not a party to the legality issue of the case, and will only be heard in terms of the decision Justice Middleton reaches.

However, in their submission, they make it clear that if the investigation is deemed to be unlawful, then the show-cause notices should be deemed invalid.

The case before Justice Middleton has been set down to last three days. It could be at least another month before he releases his verdict.

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* Key dates in the supplements scandal:

January 31, 2013: Andrew Demetriou and Gillon McLachlan meet with ASADA and the Australian Crime Commission. McLachlan asks: "Is it Essendon?" The ACC's Paul Jevtovic replies: "Say no more."

February 5: Essendon self-reports. A joint investigation between AFL and ASADA announced.

February 9: During a meeting between Essendon, the AFL and Aurora Andruska, it was mentioned that the "PM wants it to end".

March 1: Lawyer Chris Pollard questions legality of the investigation.

May: Interviews of players begin.

June 4: It emerges McLachlan wants investigation completed by August. McLachlan raises concerns about the sale of $1 million worth of finals tickets.

July 18 or 19: AFL integrity chief Brett Clothier given access to the interim report.

July 31: Essendon lawyers express concerns about the release of the interim ASADA report.

August 2: ASADA officially tables the interim report.

August 15: ASADA does not want the AFL to use the report to lay charges against Essendon. AFL responds days later: "With respect, this position is incorrect as a matter of law." It is alleged that James Hird is to be "isolated" over his objections.

August 19: ASADA and AFL call a "truce" to their deteriorating relationship.

August 27: Hird is suspended for 12 months and the Bombers fined $2 million and thrown out of the finals. Football chief Danny Corcoran is suspended and Mark Thompson fined.

June 12, 2014: ASADA issues show-cause notices to 34 current and former Essendon players.