Ivan Cleary was urged to reflect on his criticism of referees in a long conversation with NRL boss Andrew Abdo before the Penrith coach was whacked with a $20,000 fine on Monday.
Cleary is facing the hefty fine after the NRL served him with a breach notice for questioning the integrity of referees following Saturday's match against Canberra.
Cleary claimed Canberra were "managed" back into the game by officials after several second-half calls went in the Raiders' favour.
The Panthers held on to win 28-12 and his post-match comments were labelled "deplorable" by ARL Commission chairman Peter V'Landys.
On Monday, the NRL issued Cleary with a breach notice for his claims against match officials, with acting chief executive Andrew Abdo backing V'Landys' stance.
"I am disappointed that a person in a leadership position within our game has made comments that question the integrity of our officials," he said.
"Our leaders should be professional and set the standard for our game.
"Comments like this will not be tolerated."
Abdo said he had a lengthy discussion with Cleary over the phone on Sunday night before the fine was announced on Monday morning.
"I think he understands the onus and responsibility that comes with the leadership position and I certainly think he's reflected on the choice of his words accordingly," Abdo said.
In a statement released late on Monday, Cleary said he would be "submitting a formal response" to the NRL breach notice issued.
"While that process runs its course, I wish to clarify it was never my intention to question the integrity of the referees," he said.
"I will not be commenting further on this matter until it is finalised."