The under-pressure manager claimed his side were "playing against officials as well as the opposition" and said decisions given against his team were "laughable"
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"We're having to play them [the officials] as well as the opposition at the moment," the Scot said. "It's really terrible, it really is. We're actually beginning to laugh at them, that's the thing."
A statement from the FA read: "Manchester United manager David Moyes has been charged for misconduct by the FA in relation to post-match media comments he made following his side’s game against Sunderland on Tuesday 7 January 2014.
"It is alleged the comments called into question the integrity of the match officials appointed to that fixture and/or appointed to Manchester United fixtures generally, and/or implied that such match officials are motivated by bias; and/or brought the game into disrepute, in contravention of Rule E3(1).
"Moyes has until 18:00 on January 15, 2014 to respond to the charge."
Moyes is likely to face a similar fine which was given to Liverpool manager Brendan Rodgers on Thursday.
The 40-year-old was fined £8,000 by the FA for questionning the decision to appoint Bolton-born referee Lee Mason for his side's 2-1 defeat against Manchester City on Boxing Day.
"Hopefully we won't have a Greater Manchester referee with Liverpool-Manchester games in future," Rodgers said.