The Australian Football League (AFL) said on Wednesday it was investigating "serious allegations" about the mistreatment of indigenous players, including one in which coaches urged a player to have his partner's pregnancy aborted.
Clarkson, who was head coach at Hawthorn for 17 seasons until last year, released a statement on Wednesday evening saying he was "shocked" by the allegations.
"The health, care and welfare of our players, staff and their families were always my highest priorities during my time at Hawthorn Football Club," it read.
"I was not interviewed by the authors of the report commissioned by the club, and nor have I been provided with a copy of the report.
"I was not afforded any due process and I refute any allegation of wrongdoing or misconduct and look forward to the opportunity to be heard as part of the AFL external investigation."
The allegations were contained in an independent review commissioned by Hawthorn and reported by the Australian Broadcasting Corporation (ABC).
Fagan, who left Hawthorn after the 2016 season to coach the Brisbane Lions, released a statement on Thursday saying he was "shocked and deeply distressed" by the allegations and would "defend" himself.
"I deny, categorically, the allegations of wrongdoing by me in relation to First Nations players at the Hawthorn Football Club," it read.
"I have had very positive relationships with (indigenous) players throughout my many years in football, and, indeed players from different racial and ethnic groups.
"I intend to participate fully in the investigation and look forward to being heard and being accorded due process and fairness."
The players who alleged the mistreatment were not identified in either the Hawthorn review or in the ABC report.
One player said Clarkson and Fagan were among Hawthorn staff who urged him to "get rid" of his unborn child and separate from his partner, according to the ABC.
Clarkson was due to formally take over as head coach of rival team North Melbourne in November but said he had agreed to step back from his responsibilities at the club to focus on the investigation.
Fagan has also stood down from his duties at the Lions to cooperate with the AFL probe.
The emergence of the review has overshadowed the lead-up to the biggest day in the AFL calendar, Saturday's Grand Final between the Geelong Cats and Sydney Swans.
