The Blues centre-back was adjudged by by referee Martin Atkinson to have fouled Villa striker Gabriel Agbonlahor in the penalty area eight minutes from the end of the recent game at Villa Park and James Milner converted the resulting spot kick to give Villa a 1-0 win.
Johnson told the media after the match: "The referee was a disgrace. He's ruined the match and clearly shouldn't be doing these kind of games - it was too big for him."
A statement on the FA's official website reads: "The FA have today charged Birmingham City FC's Roger Johnson relating to media comments made after his side's fixture at Villa Park on 25th April 2010.
Johnson has been charged on two counts, relating to his comments about the match referee and for his comments about The FA Respect programme.
Johnson has until 20 May 2010 to respond to the charge."