Michael Cheika slammed referee Romain Poite and the Australia head coach felt New Zealand's Owen Franks was guilty of eye-gouging in a 29-9 victory for the All Blacks which ensured they retained the Bledisloe Cup.
Israel Dagg scored two first-half tries, while Julian Savea and Sam Cane touched down after the break as the All Blacks beat the Wallabies at Westpac Stadium on Saturday.
Cheika was unimpressed with the standard of officiating from Poite and the Australian Rugby Union is reportedly set to lodge an official complaint with World Rugby after the Frenchman met with New Zealand coach Steve Hansen before the game, which the Australia boss had not been made aware of.
"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 past year," said Cheika.
"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 a good opportunity for me to talk to you?'.
"He just ignored him. He's got the whistle, I understand, but there's a place where that guy, the captain, has an opportunity to speak with the referee. The referee might 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 think that attitude showed right through. I don't know if it's subconscious or not, but it's there. It's got to be dealt with, because it can't be that the opponent can have every player discussing with the referee.
"It's pretty blatant to anyone listening to the referees."
Cheika also expects action to be taken against Franks after the prop made contact with Wallabies lock Kane Douglas' face.
"We saw it at the time," he said.
"I'm sure the match review [officer] will pick that up. It was pretty open, it would be pretty hard for the match review guy to miss."