In a fiery post-match tit-for-tat with Souths coach Jason Demetriou, Payten claimed the Rabbitohs had manipulated on-field checks of players to control the momentum of the match.
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Payten was particularly unhappy with the on-field check of Rabbitohs' prop Tevita Tatola when Souths led 14-10 with seven minutes to play.
The Cowboys were just about to go on the attack from a 10-metre scrum following an error, only for play to be stopped so Tatola could be given a once over by trainers.
Tatola was also given a concussion check in the first half after the forward was hit in the ribs by a hard tackle from Jason Taumalolo.
"The game went for two hours tonight," Payten said.
"I'm very confused about one at the back-end. There was one in the first half where Jase actually hit Junior Tatola through the ribs and there was an HIA.
"That's bending the rules at best. There was one when we forced an error, there was a scrum, it was our ball and momentum was in our favour.
"It was another opportunity where they could stop the game, they get their gas back and it halts all momentum in our favour. I'd like the NRL to look at it."
Tatola later clarified that the second-half check had come after he copped an errant knee to the head from Luciano Leilua three minutes earlier.
"Luc sort of kneed me in the head," Tatola said.
"I was trying to make a tackle and his knee accidentally hit me in the head. I was a bit dazed for a sec but I was sweet."
When told of Payten's comments, Demetriou was unimpressed.
"I think he (Payten) has made a bit of a habit out of complaining about stuff," Demetriou said.
"Our medical team are as diligent and respectful of the rules as anyone in the game.
"I think if you looked at how much HIAs we've used and how many blokes we've brought off the field, we'd be one of the fewest in the competition.
"I'm going to stick up for my staff. They don't do that unless they know there's a reason to do it."
Confusion over Coen Hess-Campbell Graham incident
There was also confusion as to why Campbell Graham didn't go off for an HIA late in the game after Coen Hess was sin-binned for high contact on the Souths centre.
Payten questioned whether there was any contact with Graham's head given the fact he didn't need an HIA, however replays did appear to show Hess' shoulder colliding with the centre's head.
"There was contact with my head, I felt," Graham said afterwards.
"The initial bit I was dazed but I came good pretty quick.
"I don't know what made contact with my head. I heard it was a head clash, I know he was rattled.
"I don't have anything against it or anything, it's just one of those incidents. I don't make the decision to send him in the bin or whatever."
The win wrapped up a top-eight spot for South Sydney, and left North Queensland unlikely to claim second position and a home final.
— NRL on Nine (@NRLonNine) August 27, 2022
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