The Hammers boss made negative media comments towards referee Phil Dowd after his side were beaten in the FA Cup third round replay at Manchester United last week.
A penalty via handball from United defender Rafael was missed and Allardyce is so certain his team was harshly done by that he has denied the charges.
"The comments followed his side's FA Cup with Budweiser third round replay against Manchester United at Old Trafford on January 16, 2013.
"It is alleged Allardyce questioned the integrity of the match referee and/or match officials in general, and/or implied that the match referee and/or match officials in general were motivated by bias; and/or brought the game into disrepute in contravention of Rule E3(1).
"Allardyce has requested a personal hearing, the date of which will be set in due course."