North Queensland's Gavin Cooper has refused to back down from claims Cronulla targeted the surgically-repaired knee of Matt Scott.
The Queensland Origin forward further inflamed tensions between the two rivals on Monday when he accused the Sharks of dirty tactics in the Cowboys' round one win last week.
It prompted a fierce response from Flanagan who defended his players and claimed no one listened to Cooper.
However Cooper stood by his comments, saying the evidence was plain to see.
"I saw what everyone saw today, there's a photo going around," Cooper told Fox Sports' NRL 360.
"The ref was right there and I had something to say at the time. There were a couple of other things, a few leg pulls here and there, a few boys in some dangerous positions.
"But I'm not going to take back my comments, I know a few guys are trying to make it more than it really is.
"I'm going to stand by what I saw and what I said."
Cooper claimed Sharks defenders attempted to twist and wrench Scott's knee in what was his first game back from a knee injury which ended his 2017 campaign after two rounds.
Flanagan said the allegations were "false and ridiculous", adding, "I don't listen too much to him (Cooper), I don't think too many do."
The Sharks and Cowboys have developed a fierce rivalry over the last five years, knocking each other out of the finals on four occasions over that period, including the Cronulla beating the Cowboys in the 2016 grand final.
Sharks back-rower Luke Lewis denied there was any attempt by his side to target Scott.
"It's ludicrous what he's come out and said," Lewis told NRL 360.
"I've got a lot of respect for the Cowboys players all the way across the park, we have a game plan to get into the legs from marker but nothing to go and twist the knee of Matt Scott and try to put him out for a long period of time."