In a press conference on Monday, Cheika said would not have been able to select fullback Israel Folau for the Wallabies after his latest "disrespectful" social media posts attacking gay people.
Chieka said Folau's latest comments crossed a line.
"We've had the discussion about it after the last time about his right to believe and our support in that," he said. "But getting out in that disrespectful manner publicly is not what our team's about.
"We've had the discussion about it and that line's then been crossed. When you play in the gold (Wallabies) jersey, we're representing everyone in Australia.
"I felt that I needed to talk to him (Folau) about why, but I haven't had that chance as yet."
Farr-Jones told Macquire Sports Radio that people make mistakes and Cheika needs a player like Folau at the World Cup.
"I think Michael Cheika's been way too premature in relation to all this.
"Does he realise he's got two other selectors? Does he realise or has he consulted Scott Johnson who's just come into the fold who I think Cheika reports too, has he consulted with Michael O'Connor in relation to this?
"If I was Raelene Castle, I'd be calling Cheika into my office and be saying this isn't resolved yet.
"How on earth can you make that comment?
"I think Cheika has come out way too early and if I was Castle I'd be calling him in and ask how can you say that? Do you have the authority to say that and where does it leave Israel in the event that he is successful and is brought back into the team?
"I can tell you as far as our hopes in the Rugby World Cup you need someone like that."
Former Wallaby Cameron Shepherd disagrees with Farr-Jones, telling Macquire Sports Radio that Folau has come across as 'selfish'.
"He hasn't once said 'I apologise for the pressure its put on Australia as a nation or the pressure it's put on my teammates'.
"I don't think he cares, that's been the most disappointing aspect about this whole situation."
