Shiels was issued with a notice of complaint by Scottish Football Association compliance officer Vincent Lunny on Tuesday for accusing match official Andrew Dallas of "fabricating" evidence against him.
Shiels hit out last week after escaping further punishment for being sent to the stand in a Rugby Park match against St Johnstone last month, when Dallas was fourth official.
Shiels has been accused of impinging upon the character of a match official and acting against the best interests of football by making "improper comments of an insulting nature".
The Northern Irishman was cited for accusing Dallas of "outrageous fabrication" and acting in a "manipulative and devious" manner.
Scottish Senior Football Referees' Association chairman John McKendrick said: "In our opinion, ill-founded comments reported widely in the Scottish sporting media in recent days have impinged upon the character of one of our members.
"It is unacceptable that a referee should have his integrity questioned in such a matter.
"To accuse a referee of 'outrageous fabrication' is totally unacceptable."
The referees' body also took issue with the Kilmarnock manager's claim that he had been "totally exonerated".
The Northern Irishman was originally accused of misconduct at a match by dissent, adopting an aggressive attitude and by the use of offensive, insulting or abusive language.
The panel upheld the complaint, but only in respect to dissent, and decreed no further punishment was necessary.
McKendrick said in a statement: "For the avoidance of doubt, and in contrast to comments attributed to Mr Shiels, it should be acknowledged that on Thursday 13th December, and having digested the evidence submitted by Andrew Dallas, the judicial panel found Mr Shiels in breach of rule 203, misconduct at a match.
"Scotland's referees welcome the swift response by the compliance officer and now place our faith in the judicial panel to adjudicate on this unprecedented attack on the integrity of a Scottish referee."
Shiels and Dallas now look set to give their accounts to another judicial panel on January 10, with the Killie boss given until December 27 to respond to the notice of complaint.
The Kilmarnock manager is in the midst of a three-game touchline ban received for other comments made regarding match officials.