Brumbies interim chief executive Phil Thomson has settled into the role after stepping in to fill the void left by Michael Jones after he agreed to a payout to leave the organisation.

However, Thomson's links with the ARU via his role as its integrity unit manager prompted fears in Canberra's rugby ranks that his appointment was part of a bigger plan to take control of the Brumbies.

Thomson has put his ARU job on hold to steady the Brumbies ship after a turbulent two months, and he is working with coach Stephen Larkham this week to ramp up player contract negotiations.

Thomson will remain in the position until the Brumbies board can find a permanent replacement, and it is believed the board is set to engage a third-party recruitment agency to help with its search.

ARU general manager Rob Clarke declared Thomson's secondment to the capital was not part of a "Machiavellian plot" as officials try to make Australia's Super Rugby franchises financially viable.

"You need to have good, constructive dialogue about the challenges the club is facing and to collectively come up with a plan for how the Brumbies are best going to be managed," Clarke said.

"The end gain being a financially sustainable and high-performing team in Canberra for the long term. That's our goal and that should be their goal [in Canberra].

"The Brumbies have been to date our most successful team on the field in 20 years of professionalism, and we'd like them to remain successful.

"We will be encouraging the Canberra club presidents and the board to open their minds up to asking is there a better, more efficient and effective way to make sure that [success] is achieved.

"The answer is that there is and we have to get there. There's no Machiavellian plot here, we're all in alignment. We want a healthy, vibrant and profitable team in Canberra at the Brumbies, but it's just there might be a more efficient way."

There has been talk of a centralised Super Rugby model being introduced in Australia which would mirror the system used in New Zealand and all teams would report to the ARU.

That option remains on the table as ARU officials work with the franchises to develop a plan to plug the financial leaks in the game. The franchise chief executives will meet at the end of June to discuss any developments.

The Brumbies lost $1.68 million last year and the cash reserves from the $11.375 million sale of their Griffith headquarters has almost diminished.

Thomson has been brought in as a calming influence in Canberra after Jones and the board were locked in a legal battle for six weeks before the parties mutually parted ways after mediation.

His main tasks are to rebuild relationships in the Canberra rugby community while the board goes on a search for a new chief executive. The search could take up to six months.

Thomson is also working on a new contract for Larkham, and the formation of Canberra's National Rugby Championship team for later this year.

"The ARU doesn't have a plan to march into the states and take the Super Rugby teams away from them under a new model," Clarke said.

The Brumbies will return to training on Friday to start preparations for their game against the Japan Sunwolves on May 28.