O'Shea and Cockerill were left less than impressed by the performances of the officials during their sides' Aviva Premiership games against London Welsh and Gloucester respectively, and voiced their dissatisfaction. But the pair have been warned by the governing body that a repeat of their comments could lead to them being charged.
An RFU statement read: "The Rugby Football Union has written to Richard Cockerill (Leicester Tigers) and Conor O'Shea (Harlequins) warning them as to their future conduct in regard to comments about match officials made after the Aviva Premiership matches against Gloucester and London Welsh respectively."
The statement continued: "We have urged both directors of rugby to use the existing agreed feedback process and reminded them that questioning the integrity of referees in future may lead to their being charged with bringing the game into disrepute under RFU Rule 5.12."
Cockerill had vented his frustrations after the Tigers beat Gloucester 17-12 at Welford Road on December 29. Cockerill criticised referee Andrew Small for only sin-binning Gloucester tighthead Shaun Knight, when the Leicester boss felt his side had dominated the scrum area.
After the match, former England hooker Cockerill said: "I am lost for words. I have spent 30 years in the middle of scrums. I coach it every day. We try to be really professional and then we have to deal with that. It's just not good enough. It has got to end, enough is enough.
"He (Small) needs to look at it and see his faults and try and improve. That's the whole point of coaching, whether you are a referee or a rugby coach. (The) points (for the win) are great, you have to win these games. If you get beaten I don't mind, but I want the rugby to decide, not the bloke in the middle making poor decisions."
O'Shea, meanwhile, was left fuming over the performance of referee Llyr Apgeraint Roberts during Quins' 31-26 win at London Welsh on January 6.
"I'm unbelievably frustrated, you'd have to go a long way to see worse," he said of Mr Roberts' display. "Everything was wrong - it was incredible. The offside line was irrelevant, trailing runners coming back was irrelevant, backing into the maul, not releasing in the tackle - all irrelevant.
"We were 21-6 at half-time but bafflingly the penalty count was against us, how that can be? We have a feedback process for the referees but it's not actioned upon and it's very difficult at times."