But the ACT Supreme Court has given the Brumbies board the green light to terminate Mr Jones' contract, so long as it is not related to him making disclosures about irregularities with the sale of the club's Griffith headquarters and move to the University of Canberra.

The decision sets up a potentially explosive meeting at the Brumbies' headquarters on Thursday night, where board members and voting members will attend an extraordinary meeting.

ACT Supreme Court Justice Richard Refshauge ruled in Mr Jones' favour and added that he was satisfied that the public interest disclosures were a "dominant factor" in board's decision to stand down Mr Jones on March 21.

The EGM scheduled for hours after the ruling has two agenda items - one to dissolve the board and the other to elect new directors - and is the ACT Supreme Court decision is set to see ugly in-fighting continue at the Brumbies.

Mr Jones will remain in charge of the Brumbies despite the board trying to strip him of his duties in the wake of a fiery radio interview last month, during which the chief executive attacked his detractors and said things would "get ugly" if he went to war.

The Brumbies board is now free to take action against Mr Jones if it does not relate to the public disclosures and it gives Mr Jones five days written notice.

The Brumbies board met on Thursday to discuss its options in reference to Mr Jones' position.

Mr Jones said outside the ACT Supreme Court: "Now the question is for [chairman Robert Kennedy], [director Carmel McGregor] and the rest of the board to actually get in front of those people who elected them to explain what the hell has happened and what is in the documentation that they have been fighting so strenuously to keep quiet.

""There'll be a lot of questions that'll be asked about their involvement over the last seven years and hopefully this is the first step in the process of clearing up what's been a really unsavoury period for the Brumbies.".

"It's not over. There's still a long way to go, but today is the first step in that."

Asked if he was confident of being the Brumbies' long-term chief executive, Mr Jones said: "I would hope so. I moved my family here specifically to do this job on a long-term basis. I think I've been performing and doing an excellent job.

"I think I have the support of the whole organisation, [but] perhaps not the board. Some of that has been because of external influences and that's the point that I've been making all along. Time will tell.

"... Some of the tactics and things that have been done have been pretty ugly. But I'm a big boy and I've got to be professional. I'm trying not to make it about me, I'm trying to make it about the organisation and what's right for it and cleaning it up.

"... I certainly want all of the information to come out because I feel absolutely, 1000 per cent confident that once it comes out there will be a big 'ah-ha' moment for people as to what transpired in this whole process."

The board is set to be thrust into the spotlight in what looms as an intense meeting as Canberra club rugby presidents seek answers over the decision to stand down Mr Jones and issues relating to the KPMG report and sale of the Brumbies' Griffith headquarters.

The KPMG report will be made available to boardroom voting members on Thursday night before the EGM.

There has been speculation about whether the EGM adheres the Brumbies constitution, but Jones said it would go ahead as planned despite some clubs expressing their desire to withdraw support.

Mr Jones had been dealing with constant rumours about his future since December last year, when the club announced a record deficit of $1.68 million.

Tension stems from the KPMG report, which details transactions at the club between 2009 to 2013, which is part of an ongoing Australian Federal Police investigation and was jointly funded by the Australian Rugby Union and Brumbies.

The board took action to stand down Mr Jones and it is believed his contract was not terminated given the Brumbies' perilous financial state.

But Mr Jones did not leave quietly. Within 24 hours, he was in the ACT Supreme Court, using the ACT's whistleblower legislation to stymie the Brumbies attempts to stand him down.

He argued he had made disclosures in the public interest, and was the victim of detrimental action by the Brumbies board and a range of others, including former ACT deputy chief minister David Lamont, Wallabies great Joe Roff, the University of Canberra, and the UC Union.

The exact nature of what he blew the whistle on has been kept secret by the court.

 But it is understood that it relates to irregularities and concerning aspects of the Brumbies sale of its headquarters at Griffith, and subsequent move to the University of Canberra.

A KPMG report into the transactions is understood to contain explosive allegations, and is a key source of tension. The contents of the report, which is the subject of an ongoing Australian Federal Police investigation, remain suppressed by the court.

The ACT Supreme Court agreed to give Mr Jones whistleblower protection on March 22, preventing the Brumbies from standing him down, and gagging the club or the other parties from acting on or discussing his employment publicly.

The Brumbies hit back a short time later, bringing the matter back to court seeking to dissolve the injunction that protects Mr Jones.

They argued he should never have been deemed a whistleblower for a range of reasons, including that his disclosures weren't serious enough, and didn't identify any individual public official responsible. It was also argued that there was no evidence of a causal connection between what Mr Jones disclosed, and the club's decision to stand him down.

Justice Refshauge ruled in Mr Jones' favour on Thursday morning.

"Accordingly, I am satisfied that, taken as a whole, the decision of the board shows, to the relevant degree, that it was taken because of the public interest disclosures made by Mr Jones, at least as a dominant factor, and that this is sufficient to the purpose of the interlocutory proceedings," Justice Refshauge wrote.

But he also varied the orders, adding a new order that said the Brumbies board could exercise its rights to terminate Mr Jones' contract, as long it is not related to his disclosures about the Griffith sale.

"It is noted that, provided five working days' notice is given in writing to the Plaintiff [Mr Jones], the [the Brumbies board]is not restrained...from exercising any rights it may have under the contract of employment between it and the Plaintiff to terminate the contract consistent with its terms other than for any reason related to the public interest disclosures made to Professor Stephen Parker or Mr David Dawes," Justice Refshauge wrote.

Canberra club rugby presidents have called for an extraordinary general meeting to seek answers from the board about its decision on Mr Jones' future and how it has handled the proceeds of an $11.375 million sale of its former Griffith base.

Part of the sale was supposed to be used to set up a trust fund to give financial support to Canberra's club competition. But the fund was never set up and the proceeds of the sale have almost disappeared.

The club rugby presidents hold the balance of power in the Brumbies' boardroom, boasting 14 of a possible 23 votes.

Mr Jones has met with the presidents and it is believed officials have seen the contents of the KPMG report. Presidents called for the EGM with two agenda items - a special resolution to dissolve the board and a normal resolution to elect new directors.

Justice Refshauge's decision is set to turn the blowtorch on the board given it attempted to remove Mr Jones from his position a month ago.

Mr Jones was told to hand over his keys to the Brumbies office, his work laptop and had his business credit card cancelled when he was stood down indefinitely.

Brumbies chairman Robert Kennedy attended the Brumbies office the following morning to inform staff that the search for a new chief executive would start immediately.

But Mr Jones gained an injunction just hours later and was back behind the desk less than two days after the board tried to stand him down.