Fleetwood manager Steven Pressley has accused the Football Association of "washing their hands" of their complaint against referee Carl Boyeson.
The club were angered by comments they claim Boyeson made after keeper Chris Maxwell was hit by an "object" during Saturday's game with Sheffield United.
The Professional Game Match Officials Board are now in charge of the case.
"I believe if it was from a higher profile club, the FA would have been hands on," said Pressley.
"Unfortunately they have washed their hands of it and pushed it on to the committee.
"The FA have to treat every club the same and I think in this instance this is something they should have had a serious look into."
BBC Sport understands the FA considered the complaint, but were satisfied that it was not a disciplinary issue for them.
The PGMOL has also been contacted by BBC Sport but are yet to reply.
Pressley alleged after the match that the referee said the incident was Maxwell's own fault, and striker Shola Ameobi confirmed he was the "witness" to the alleged comments.
"It is sad to see when things are thrown at players," the former Newcastle striker, 34, told BBC Radio Lancashire.
"It is something that I do not condone and it is something that I feel the referee could have dealt with better.
"The comments that I heard him say weren't what you want from a referee to a player.
"It's a tough situation that the referee found himself in and the goalkeeper is there to stop goals going in not stop things bouncing off his head."