NORTH Melbourne is confident Alastair Clarkson will one day return to coaching, having informed the club on Wednesday afternoon that he would be taking indefinite leave from his role effective immediately.

Clarkson, in a phone call with his wife Caryn, told club officials this week that he would be stepping away from the Kangaroos as he continues to deal with the fallout of an investigation into allegations of mistreatment of First Nations players during his time at the Hawks. He denies any wrongdoing.

In a statement released on Thursday, North Melbourne said that Clarkson – who was due to coach his 400th game this weekend when his side plays Sydney – would be provided "whatever time he needs to restore his health". The club said "everyone involved has been deeply affected by the Hawthorn investigation and the burden on Alastair has been significant".

Speaking on Thursday, the Kangaroos' football boss Todd Viney reiterated his belief that Clarkson would return but didn't put a timeframe on when the four-time premiership coach would make his comeback to Arden Street.

"I personally don't (think Clarkson will be lost to the game)," Viney said.

"Certainly, that's a possibility, but I don't think ... I think he just needs a little bit of time. There was no indication in the conversations yesterday that it was the end of Alastair Clarkson. We feel really confident that he just needs some time to heal and he'll be back and taking control of the club again and helping us get back to the battle of contending for silverware and getting this club back to being in that position.

"There's been no timeframe to talk about when he's coming back. It's our firm belief that he will be back this year. But, if you ask him and if you ask us, we can't tell you whether that's one week or six weeks. We'll take that as it comes. The No.1 priority will be for him to get fit and healthy again. In the meantime, he will be away. We've told him to burn his phone and to just concentrate on getting himself right."

North Melbourne held talks over Clarkson's future at its Arden Street headquarters on Wednesday evening, following a meeting between the coach, his wife Caryn, CEO Jennifer Watt, football boss Viney and president Dr Sonja Hood.

It was there that Clarkson informed club officials he would be taking indefinite leave, effective immediately, a decision that Viney described as "brave". The club also made the decision to appoint former Carlton and St Kilda coach Brett Ratten, currently a part-time assistant at North Melbourne, as its caretaker coach.

Ratten will subsequently become the Kangaroos' sixth coach in five seasons, following in the footsteps of Brad Scott, Rhyce Shaw, David Noble, interim Leigh Adams and then most recently Clarkson.

"Unfortunately, we've lost our coach," Viney said.

"Late yesterday, we received a phone call from Clarko and his wife Caryn to see if he could come in and have a conversation with Jen, Sonja, myself and (his manager) James Henderson about how he's feeling both physically and mentally.

"We caught up and, in that conversation, he basically outlined that the previous eight months of what he's had to deal with in terms of the Hawthorn investigation and the serious allegations that have been made through that complaint and not having a voice for that period of time has really weighed him down in the mental space.

"He's bravely fought on through this period to be the North Melbourne senior coach and that's a really serious role in itself, one that he is fully passionate about doing and helping to build this club up to be a great club again. The reality of that is, in dealing with the previous eight months and the role as the North Melbourne coach, he felt that he just couldn't do it anymore.

"If you ask anyone in the four walls about how he'd been going, they really wouldn't have been able to tell how much pressure he was under because he's done an amazing job in building relationships and helping to set the foundation for this club moving forward.

"But when he leaves this workplace and he goes home and he's dealing with the constant unknown around this investigation, it's really taken a massive toll to the point where he just feels like he needs to get himself right before he can help his family and us as a club."

Brisbane coach Fagan released a statement on Thursday afternoon, saying he was "saddened" by Clarkson's decision to step away from football, and criticising the "deeply flawed" process around the allegations at Hawthorn. 

"I was fortunate to work with Clarko for almost nine years, and I have known him for much longer than this. I know him to be a person of very good character who has had an overwhelmingly positive influence on the lives of the young men he has coached. The football community is immeasurably better off with Clarko in it," Fagan said. 

"The deeply flawed process that we have been subjected to has taken a heavy toll. It has been profoundly damaging and unfair. It is my hope that it will very soon come to an appropriate end.

"In the meantime, Clarko's physical and mental wellbeing must come first. I extend my very best wishes to him, Caryn and his family."

AFL CEO Gillon McLachlan also released a statement on Thursday afternoon, supporting Clarkson's decision and acknowledging the "heavy burden" borne by all parties involved in the investigation. 

"We understand how much the investigation by the independent panel into allegations of racism has impacted on all people involved, including Alastair, and believe the investigation needs to find resolution," McLachlan said. 

"It is a heavy burden being carried by all parties involved and the wellbeing of everyone who is a part of this process is the key priority for our game. 
 
"It takes great courage to stand up and say you need to focus on your own personal wellbeing and we support Alastair in doing what he needs to do in the best interests of himself and his family.  We will continue to provide support to all parties.

"The AFL supports current efforts to find a mediated outcome that provides fairness and natural justice for all involved and encourage all parties to work towards a timely and just outcome."

Last week, in a revealing press conference, Clarkson called for Hawthorn to be investigated for the club's "shameful" handling of its report and said that reputations had been "scarred" as a result of the long-running process. He said the game was a "victim" of the ongoing independent investigation, which was commissioned by the AFL in October.

"I think that was a window into his mindset at the time," Viney said.

"You got a good feel for the animosity he's got towards the Hawthorn Football Club, a club that he served for 17 years and four premierships. He had such an influence on so many people within that football club.

"For the process to unfold and such serious allegations to be made and to have no reply to that process has been enormously hurtful to him. If you know Clarko, it's about relationships and it's about trust and it's about family. When he commits to being part of your organisation or family, he's in 100 per cent. To have that unfold like it has, he's been bitterly disappointed and that's taken its toll."