Godolphin has been fined STG15,000 ($A26,073) for breaching the sponsorship rules at the English Oaks meeting.
The groom handling Skiffle at the meeting in June wore a Godolphin jacket instead of one bearing the name of the sponsor Investec.
The British Horse Racing Association also found the world racing power's chief executive John Ferguson had removed tape placed over the Fly Emirates logo on jockey William Buick's silks.
The Racing Post reported the fine to be at the higher end of the scale which has a maximum penalty of STG25,000.
The BHA's Robin Mounsey said the disciplinary panel found Godolphin had flouted the rule which guarantees Investec exclusivity on Derby and Oaks day.
"The actions of Godolphin on the day were a clear and admitted breach of the rules, and it was appropriate for the BHA to pursue the matter and have the disciplinary panel consider what disciplinary action was warranted," Mounsey said in a statement.
"However, we believe there is a wider question here as to whether the sport can do more to avoid potentially conflicting sponsorship arrangements and also whether the BHA's resources are best used enforcing rules which address issues more relevant to our sport's commercial parties."
Mounsey said the executive committee would raise the topic at its meeting next month.