An email from Chris Fagan's legal representatives to the lawyer of the families central to the Hawthorn probe flagged a Supreme Court injunction and their identities being revealed, according to reports.

The correspondence reportedly led to an agreement ending the investigation into alleged serious misconduct towards Indigenous players by Fagan, Alastair Clarkson and Jason Burt, announced by the AFL on Tuesday evening.

AFL chief executive Gillon McLachlan said the investigation closed after "no adverse findings" against the trio.

All three men have denied any wrongdoing over months since the allegations emerged.

According to Herald Sun chief football writer and AFL360 host Mark Robinson, the email was sent Sunday May 28 by Clayton Utz partner Scott Sharry and senior associate Stephen Hurford to the families' lawyer Leon Zwier.

It informed them Fagan intended to launch a case in the Victorian Supreme Court in the week starting Monday May 29, and no later than Thursday June 1.

The start of an injunction against the AFL and investigation panel would have seen the families become the defendants and identified by name.

The families were given until 4pm Monday to respond.

An unnamed source described the email as a factor in the families' decision to agree to the deal with the AFL.

In a statement released following after the league's announcement to the end of the probe, Fagan said he was "glad that it has finally been brought to an end".

"I am not a party to the agreement between the complainants, the investigation panel and the AFL. But I stand vindicated by it," he said.

"I have made no concessions. There are none to make. I have always vigorously defended myself, and will always do so, as I have done nothing wrong."

Fagan reiterated his claims of innocence, and that he has "always respected the tremendous contribution that First Nations people have made to our game and I respect them greatly".

"I always have. I always will. And I am conscious that this farce of a process cannot have been easy on those First Nations people who were complainants," he said.

The Brisbane Lions coach said documents held by Hawthorn, the complainants, the AFL and investigation panel were released to him "very recently" and that he is bound by a confidentiality deed not to share details.

"I am happy for any of my conduct and any documents to be aired publicly in a public court or proper public process and let someone impartial decide what is true and what is false," he said.

"I am not a party to the agreement between the complainants, the investigation panel and the AFL. But I stand vindicated by it.

"I have made no concessions. There are none to make. I have always vigorously defended myself, and will always do so, as I have done nothing wrong."

The email from Fagan's representative on May 28 reportedly said: "The purpose of this letter is to notify your clients, pursuant to…the Deed, that..our client intends in the week commencing 29 May 2023, and no later than Thursday 1, June 2023, to commence a proceeding in the Supreme Court of Victoria for orders in the nature of permanent injunctions restraining the continuation of the investigation."

"The proceeding referred to above will include each of your clients as defendants, identifying each by name, on the basis that they are (with others) necessary parties because they are directly affected by the relief to be sought. The proceeding to be filed will not disclose any "information" as defined in the Deed concerning your clients other than their names.

"As the proceeding progresses, however, additional 'information' will be disclosed as part of the proceeding. Your clients will be notified in advance of each disclosure pursuant to the Deed."

In the email, Fagan's representation is understood to have said "we consider there to be no reasonable basis for your clients' names not to be disclosed in the proceeding to be filed by our client" but invited the families to explain any "contention and their proposed course of action by 4.00 pm on Monday, 29 May 2023".

"In the absence of this our client will proceed on the basis that your clients do not disagree with our client's position."

The families reportedly discussed the email in a crisis meeting with Zwier on Monday.

One family is understood to regret agreeing to the AFL's deal to end the investigation, feeling they were used as a "pawn", as described by the Herald Sun, in actions to end the months-long probe.