Spaniard Martinez was dismayed at the decision to award United a penalty when Michael Oliver, the Premier League's youngest referee at 27, pointed to the spot after Danny Welbeck went down under pressure from goalkeeper Ali Al-Habsi.
"Roberto Martinez has been charged by the FA for media comments made after his side's Premier League fixture at Manchester United on 15 September 2012," the FA said on their website on Wednesday.
"The charge is in relation to an alleged breach of FA Rule E3 concerning media comments which implied that the match referee and/or match officials in general are motivated by bias and/or brought the game into disrepute," the statement added.
The Wigan boss also felt England man Welbeck should have seen red for his late rash challenge on Franco Di Santo but it was his reaction to the fourth-minute penalty, which Al-Habsi saved, that has landed him in hot water.
"The penalty was as bad a decision as you are going to see in the Premier League. You know what he's trying to do. If you see the replay, you will see what I'm trying to say. It was a shocking decision. He dived," said Martinez.
Martinez, whose side travel to Sunderland on Saturday, has until 15:00 GMT on Thursday to respond to the charge.
