A day after Clarkson, arguably the greatest coach in Hawthorn's history as a four-time premiership winner, unloaded on the Hawks, Fagan backed up his friend's thoughts in less explosive fashion.
"This investigation's been going on for eight months and we haven't had a chance to tell our truth, but every week we have to put up with articles being written about it," Fagan said in Brisbane on Friday.
"Our names being almost slandered, to some degree, that becomes difficult so I understand where he's (Clarkson) coming from."
Clarkson, Fagan and Jason Burt have been named as figures involved in an alleged episode of racism during their time at Hawthorn between 2008 and 2016.
All deny any wrongdoing.
The three men are yet to be given an official right to respond to the damning allegations, even during the initial review conducted at Hawthorn by Phil Egan.
On Thursday, Clarkson blasted Hawthorn's conduct as "shameful" and believed reputations had been "scarred".
The North Melbourne coach also slammed panel chairman Bernard Quinn KC for releasing some details of the process to the media despite conditions around confidentiality.
Fagan said he was in "good health" with the support of his family and the Lions.
"The thing about it is I have a clear conscience so I'm sleeping well at night and they're the only bits that I can control," he said.
"Hopefully things can be sorted out in the most fair and just way down the track, I'm just not sure when that will be.
"I don't live my life thinking about it, day in, day out."
Former Hawthorn president Jeff Kennett has called for the AFL "to close the thing down", but outgoing AFL chief executive Gillon McLachlan said it was too early to set a deadline about when the investigation would end.
The AFL originally wanted to complete proceedings before Christmas last year when the allegations first surfaced in September.
"We have got to have people to get to the point - if it's at a point where there is a total impasse, at some point decisions have got to be made. But we are not there," McLachlan told 3AW on Friday.
"It's really important that this independent panel get to the end and I am hopeful that people can talk and find a way through. It is incredibly difficult.
"They are incredibly serious allegations and the way the process has played out, it has taken a huge toll on both sides."
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