The 29-year-old, who was 20th man for the Maroons in their 24-12 win, spoke the morning after the win and said "the game's rorted", and referred to Klein as a "double agent".
Dolphins prop Kerr, who likes to crack jokes, had his tongue in cheek with the comments, but they were not well received by the NRL.
NSW won the penalty count 7-3 after the Maroons had led that statistic 10-2 in their 26-24 win in game two.
On Saturday, the NRL issued Kerr with a breach notice alleging a breach of the NRL Code of Conduct.
"The comments are considered detrimental to the best interests of the game and also serve to undermine the credibility of match officials," the NRL said in a statement.
Kerr, in the afterglow of the 2-1 series win, was interviewed by reporters early on Thursday morning after the Maroons celebrated their victory.
"I'm not sure how much trouble I could get into for saying it, but I thought Ash Klein did a bit to try and ... even it up or make it a bit closer," Kerr said.
"We were sitting there (on the bench) going, 'it's rorted, the game's rorted'.
"I haven't got the best eyesight at times, but I'm watching forward passes and shit. We were all on the sideline going, 'oh no, it's a double agent'.
"It makes it more exciting, doesn't it, and it brings out the Queenslander in all those players."
Kerr has until Friday to respond to the breach notice.
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