Veteran Australian Rugby Union (ARU) boss John O'Neill believes the time was right for him to stand down with the move leaving his successor to oversee some crucial issues facing the Wallabies.

O'Neill announced his resignation as managing director and chief executive on Friday after 14 years and two terms with the 61-year-old to concentrate on his business interests.

The decision comes at a tough time for the Wallabies with uncertainty over the future of coach Robbie Deans and the unresolved matter of Quade Cooper's claims the environment in the national team is "toxic".

Cooper's comments have caused unrest among players and officials.

ARU chairman Michael Hawker jumped in when the departing CEO was asked a question regarding Cooper at the press conference on Friday.

"I think Quade's situation is in Quade's backyard and it's got nothing to do with John," Hawker said.

"I don't want this to become a press conference about Quade. This is a press conference about the ARU and John and his contribution to the game."

O'Neill's decision came earlier than he'd originally forecast, having said in the wake of the Wallabies' semi-final elimination at last year's World Cup that he would not continue beyond the end of 2013 when his contract expired.

But he finishes on October 31, allowing him to focus primarily on his role as the chairman of casino operator Echo Entertainment Group.

"I've just reached the point, and age has a little bit to do with it, I've turned 61 this year," O'Neill said.

"Being a full-time chief executive is not something that is really for me (now) and it's better to be honest about it.

"Fourteen years is a long time for one person to have run an organisation in any industry."

O'Neill said he and Hawker agreed to bring forward his departure date while on the Wallabies' recent trip to South Africa.

He first had the job from 1995 to 2003.

In March 2004 he took charge of Football Federation Australia before returning to the ARU in 2007.

O'Neill and the ARU board controversially re-signed national coach Deans for a further two years before last year's World Cup, so the New Zealander could take the side through to the British and Irish Lions tour of Australia next year.

Deans's contract was to expire at the same time as O'Neill's.

The decision to stand down means O'Neill has ruled himself out of choosing between Deans and the popular Ewen McKenzie as Wallabies coach for the next Rugby World Cup campaign.

ARU deputy chief executive Matt Carroll will be caretaker CEO while a global search is conducted for a long-term replacement.

O'Neill was a major contributor to Australia's golden era between 1998 and 2001, which included winning the 1999 World Cup.

He also led the planning for the 2003 World Cup in Australia before moving on to the FFA for a three-year stint where the A-League was established and the Socceroos qualified for the FIFA World Cup for the first time in 34 years.

"I've got so many good memories. Luck and timing in life always plays a significant role and I've been very lucky," he said.