Rioli is the lead applicant alongside his wife Shannyn Ah Sam-Rioli, former players Carl Peterson and Jermaine Miller-Lewis, his partner Montanah-Rae Lewis, and Hawthorn's former Indigenous liaison officer Leon Egan.
The step comes after mediation between the group and those accused of racism - including former Hawks coach Alastair Clarkson and his assistant Chris Fagan - was terminated by the Human Rights Commission in May.
The Hawthorn Football Club is listed as the sole respondent in the Federal Court documents, while Clarkson and Fagan were not specifically named.
Hawthorn commissioned a cultural safety review in 2022 to investigate allegations of systemic mistreatment of First Nations players at the club.
The findings were made public via a media report in AFL grand final week that year.
An AFL investigation later found no adverse findings against Clarkson, Fagan and former Hawks welfare manager Jason Burt.
Alastair Clarkson and Chris Fagan have denied any wrongdoing including allegations of racism. (Julian Smith/AAP PHOTOS)
Clarkson, Fagan and Burt have consistently denied wrongdoing and rejected accusations of racism.
On Friday, before the Federal Court documents had been lodged, current Hawthorn coach Sam Mitchell was asked by reporters for his reaction to the likelihood of the step being taken.
The documents were lodged before the deadline on Friday afternoon.
"As we have done throughout this process, we will continue to work towards a resolution in a fair and timely manner for all parties," Hawthorn president Andy Gowers said.
"The Federal Court process will importantly give Hawthorn Football Club the opportunity to respond to these allegations.
"Given the matter is now before the courts, it would be inappropriate to make any kind of comment that could impact on that process."
Current Hawthorn coach Sam Mitchell was a teammate of the three players listed as applicants, and played in four premierships alongside long-time teammate Rioli.
In June last year, Mitchell said it would be up to Rioli whether he would mend relations with the club, and hoped to speak with his former teammate about the "ordeal".
On Friday, Mitchell chose not to confirm whether he had spoken to Rioli or anyone involved.
"If I have reached out and spoken to these people, I don't feel like I would say that publicly - whether I have or haven't - because that's a private conversation," Mitchell said.
"It's very difficult when you're doing two press conferences a week to keep your private life private, but I have, as much as I could, tried to keep the private conversations that I have with anyone private.
"What I hope happens is everyone feels heard and we can get to the end of this process with a bit more clarity than we have right now."
