AFL commissioner Kim Williams has declared the league conducted the investigation into the Essendon supplements scandal "responsibly and professionally", and has taken aim at how the former Labor government handled what was dubbed the blackest day in Australian sport.

As the Bombers and coach James Hird attack the manner in which the probe by the AFL and the Australian Sports Anti-Doping Authority last year was handled, and the 34 Essendon players issued with show-cause notices seek to have them revoked, Williams, who joined the AFL Commission only in January this year, said the AFL and NRL, the latter through its scandal involving the Cronulla Sharks, had been forced to carry the "follow-up burden" once the drug investigations were made public.

"As a new AFL commissioner, I can't comment on the Australian Sports Anti-Doping Authority and the Australian Crime Commission dealings in 2013," Williams said.

"It is difficult, however, for the community to fathom how so much mud was thrown with such gravity, and yet there has been so little evident official follow-through. The dealings give every appearance of being what used to be colourfully described as a muddle. Thus far, it demonstrates that the agencies did little to properly manage their processes and investigations and the sports seem to have shouldered most of the proper enforcement and follow-up burden.

"It has been an ignoble moment for government bodies generally and has done much damage to Australia's international sports reputation - the announcements about issues and investigations into the taking of banned substances in various codes of football in February of 2013 gave every appearance of having been hasty and underprepared."

Williams made his comments in his just-released autobiography, Rules of Engagement. He has become the first AFL commissioner outside of former AFL chief executive Andrew Demetriou, current chief Gillon McLachlan and commission chairman Mike Fitzpatrick to publicly comment on the investigation.

"The issues are immensely serious and the actions which followed from the AFL in particular were handled responsibly and professionally, however the political and administrative grandstanding can be seen for that it was - grubby baseline politics of the lowest order, with little regard for reputational damage nor for effective applied sanctions," he said.

"One trusts there is a lesson here for the long term on administrative and communications action. Mud is sticky stuff."

Prime Minister Tony Abbott last week labelled the so-called blackest day in Australian sport as an "absolutely pathetic" attempt by the previous Labor government to deflect attention from its own woes.

In February last year, Labor ministers Jason Clare and Kate Lundy, flanked by sports chiefs such as Demetriou, held a media conference detailing the findings of a year-long anti-doping investigation by the Australian Crime Commission. This focused on links between drugs, match fixing and organised crime, prompting former ASADA chief Richard Ings to label it the blackest day in Australian sport.

The Federal Court case brought by Hird and the Bombers against ASADA has revealed the extent of pressure former anti-doping chief Aurora Andruska was put under by the Labor government to later speed up the investigative process, with Lundy allegedly requiring a "deal" with the AFL. Hird and the Bombers argue the investigation was unlawful as ASADA should have acted independently.

While Williams and Abbott were critical of the former government, ASADA responded in its own way last week when 10 current NRL players accepted a deal that has resulted in a backdated 12-month suspension for their involvement in the supplements program at the Sharks in 2011. The players were given a compelling 30-page document by ASADA before their final admissions, highlighting the strength of the anti-doping body's case against them.

McLachlan said on Friday the AFL saga "was a challenging period with the scrutiny and the way things play out" but all parties were waiting on Justice John Middleton to make his decision on whether the AFL and ASADA investigation was unlawful. A decision on whether the Bombers and coach James Hird are successful is expected within weeks.

"Essentially, everything is in a holding pattern until then," McLachlan said.

"He will make a decision on whether some or all the evidence was illegally gathered. ASADA have other evidence that they would use (if Middleton rules in favour of Essendon and James Hird). I don't know where it goes once he makes a decision. The uncertainty is incredibly difficult."