Reading boss Steve Coppell and Blackburn chief Mark Hughes want the FA to provide clear direction on their "respect for officials" campaign.
The FA this month launched a £200million grass-roots initiative with new chairman Lord Triesman urging the professional game to lead the way in an issue which "continues to scar football".
But he was forced onto the defensive after Nicky Shorey, infuriated as Coppell was by an inconsistent performance from referee Mark Clattenburg and his assistants in Saturday's clash between the Royals and Rovers, was booked for dissent.
He then suggested to Lord Triesman that if professional clubs are expected to take the lead, perhaps the FA ought to get in touch.
"My opinion is the referee is right when he is wrong but in the heat of battle over 90 minutes, players play with passion, they are required to perform and if they see blatant poor officiating then questions have got to be asked," said Coppell.
"I would prefer they weren't asked at the time of the incident. The performance of the officials will be reviewed and we should just let that happen.
"But with 24,000 people here and so many jobs at stake; if a club gets relegated an awful lot of people lose jobs. We have a responsibility to try and protect our own people.
"It is human nature. When you see an injustice, you stand up. Do you want to be the silent majority and let it float by or do you stand up? Most people do stand up."
Coppell said he spoke to Clattenburg before kick-off and was told there had been no directives from on high about curbing dissent, despite the pronouncements from Lord Triesman and football development boss Sir Trevor Brooking.
"I haven't heard a dicky bird from the FA," said Coppell.
"I don't even know who the fellow is. Lord who? Do you not think he should have made contact with someone from the professional game?"
Hughes agreed with Coppell that the issue of players reacting in an "emotive sport" is not going to be stamped out overnight.
But he called directly on the FA to clarify what has become a muddled situation over the last fortnight.
"It is not going to happen overnight. I have been playing the game for 30-odd years. It was the same when I started playing and when I finished," said Hughes.
"We probably need a statement from the main body - be it the FA or the Professional Game Officials - so everybody knows where they stand with rulings, what is tolerated and what isn't.
"At the moment it is a grey area. Nobody is sure if there is a directive out there. Maybe if the FA come out with a statement saying this is how the game is going to be refereed that will help."
