Shiels has until December 27 to respond to the notice of complaint and his hearing will be at Hampden on January 10, when he will be asked to explain comments he made about fourth official Andrew Dallas.
Shiels is already serving a three-game touchline ban and faces a longer one for saying that Dallas had "fabricated" evidence against him and been "manipulative and devious" during an earlier SFA hearing on December 13. The new notice of complaint could result in Shiels being found guilty of breaking the rules which prevent managers from questioning the character of a match official, as well as making comments not in football's best interests.
The episode stems from a game between Shiels' Kilmarnock, and St Johnstone, in November in which Shiels became involved in an angry exchange with Dallas after his captain, Manuel Pascali, had been sent off by referee Euan Norris. At Hampden last week, he received a five-game touchline ban, two suspended.
Shiels had said the touchline ban was "morally wrong" and said that Dallas had "fabricated stuff to try and incriminate me", adding "the fabrication was outrageous". Dallas later said he was "surprised and disappointed" by Shiels' accusation and would seek advice from the Scottish Senior Football Referees' Association.
If the new complaint is upheld against Shiels, the suspended element of the five-game punishment may be activated. In addition to other games it could leave the Killie manager with a touchline ban of more than 10 games.