The Australian Rugby Union will make an official complaint to World Rugby in a dramatic aftermath to Australia's 14th straight Bledisloe Cup defeat.
Cheika suggested referees have predetermined ideas about his players and was left fuming by the refereeing performance of Romain Poite in Wellington as Wallabies skipper Stephen Moore struggled to get communication from the official.
The ARU will make an official complaint to World Rugby's integrity unit over a meeting between the Poite and All Blacks coach Steve Hansen before the Test, without their knowledge or invitation.
Under World Rugby rules, coaches are not allowed to meet with referees before games unless their opposition is given notice and the chance to also attend.
The Wallabies will allege Hansen met Poite without telling them, which would breach the law 15.4.2 which reads: "Any meeting with the referee involving participating Unions before any International Match, may only take place if a representative of both Unions involved in the Match is present, unless one of the Unions, having been offered the opportunity to attend a meeting with the referee elects not to do so, in which case the meeting may proceed with a representative of only one participating Union present."
The Wallabies refused to comment on the situation on Saturday night.
"I was bitterly disappointed to be honest, I'm on record with the referees' boss Alain Rolland about the treatment to our captain and to our players by Romain Poite and also by Nigel Owens over this last year," Cheika said after his side's 29-9 loss.
"I'm not quite sure why, but there was a time there in the game, in a break in play, where the national captain of Australia was asking the referee, 'When might be an opportunity for me to talk to you?' And he just absolutely ignored him.
"He's got the whistle, I understand, but there's a place where that guy, the captain, has an opportunity to speak to the referee.
"And the referee may not like the captain personally, that might be his prerogative, but he has to afford him that opportunity if he's affording it to his opponents.
"I don't know if it's subconscious or not, but it's there, it's got to be dealt with because that can't be going on.
"I don't know if they've got predetermined positions on our players, I asked Alain Rolland, I saw him last week in Sydney, and he said 'No, that's a surprise to me if that is'.
"But it's pretty blatant to anyone listening to the ref's ears."