The Cowboys will play Cronulla away in an elimination final on the back of a 50-30 thrashing by Canberra, that got off to a horror start for the hosts in Townsville when lock Cotter was sin-binned for a high shot on the retiring Raiders legend after just 15 seconds.
Referee Nick Pelgrave said it was reckless and forceful to the head, but Papalii passed his HIA and returned to go out a winner.
Payten said he was not resigned to losing Cotter for the Sharks showdown.
"Not necessarily. It was a big collision, definitely," Payten said.
"Watching it again a couple of times, I thought it was head on head.
"I thought Papa stayed down just in disappointment of dropping the ball, and then in the HIA he was cleared and came back to play which was a good thing for him and a good way for him to finish off his career."
Cotter was of the same view on the hit and also said it was "head on head".
The 27-year-old has already been charged three times, all grade one, by the Match Review Committee (MRC) this year, but has no extra loading on his record ahead of playing Cronulla next week.
Two of the charges have fallen off his record given they were more than 10 weeks ago and he successfully challenged a high shot charge on Gold Coast's Jayden Campbell in round 23.
A grade two charge will see him suspended for the Sharks clash.
North Queensland were way off the pace against Canberra and conceding 50 points heading into finals was not what the coach wanted.
"Shocked, very disappointed," Payten said of the display.
"But it is a new competition next week, and we have got to get past that quickly and dive into what we are doing on Monday."
The Sharks have also limped into the post-season, but the Cowboys must find defensive resolve and fix their discipline if they are to go further than week one of the playoffs.
"We have got to look at ourselves," Payten said.
"That is four games in a row that we have had someone in the bin through poor discipline or a stupid decision and that is all in our own control.
"The game is too hard to play with 12 men. We do that next week and the game is gone.
"It is about high completions and field position in the next four weeks and if you don't get any of them right then you are not in the contest."
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