"It's disappointing it's taken this long but is anyone surprised? This is the game we're in, it's been like this for a long time," Fardy said.
"The officialdom in this game has always been like that."
While the ARU has come under fire for their handling of the process, the Test back-rower said Super Rugby's governing body lacked a public face.
"Obviously everyone looks at the ARU at the moment but you wouldn't know who the head of SANZAAR is at any point - I wouldn't know what he looks like," Fardy said.
"In other sports, especially in Australia, you have a head we can look at. In SANZAAR rugby we don't know who is running it.
"It's faceless men in suits in board rooms."
Fardy, who is leaving the Brumbies at the end of the season to join Irish powerhouse Leinster, said he felt for Force and Rebels players, as well as others affected by a moratorium on contract talks for non-Wallabies.
"It's guys' livelihoods," Fardy said.
"It's incredibly tough for players to have go through that."
He said he supported the Rugby Union Players' Association's position of backing five Australian teams, but accepted Super Rugby needed structural change.
"I'm hoping that with all that stuff we get change so we're not having these conversations in five or ten years' time," Fardy said.
"Hopefully we see changes for the benefit of rugby and this competition gets better from it."