The 21-year-old has until 6pm on Wednesday to respond to the charge, which relates to an incident in which he appeared to catch Scott Parker's head with his foot during Sunday's 3-2 Premier League win over Tottenham.
An FA statement read: "The FA has today charged Manchester City forward Mario Balotelli with violent conduct following an incident in his side's home game against Tottenham Hotspur.
"Balotelli was involved in an incident with Tottenham's Scott Parker during Manchester City's 3-2 victory at the Etihad Stadium on Sunday 22 January 2012.
"Balotelli has until 6pm on Wednesday 25 January 2012 to respond to the charge."
The one consolation for City is that Joleon Lescott will face no further action for catching Younes Kaboul in the face with his forearm in a separate incident at the Etihad Stadium.
If he accepts his charge, Balotelli will miss the Carling Cup semi-final second leg against Liverpool at Anfield.
However, should the Italy international decide to appeal he will be free to face the Merseyside giants, with a hearing taking place later this week.
It would seem, though, that Balotelli would be at risk of getting the suspension extended if he took that course of action as referee Howard Webb informed the FA today that, had he seen the Italian's apparent stamp, he would have sent the City player off.
It is a view widely shared across the game, with a succession of former players and managers arguing that Balotelli should have been sent off.
That he went on to score the injury-time penalty that gave City their win, only heightened Harry Redknapp's discomfort immediately after the game.
"I don't like people kicking other people in the head on a football pitch," said the Tottenham boss after the game.
"It is not something I understand. Why should he go and back-heel someone in the head when he is on the floor?"
If he accepts the charge, Balotelli would also miss the Premier League trips to Everton and Aston Villa, plus the home encounter with Fulham on February 4.
It is the latest in a long line of disciplinary issues involving Balotelli since his arrival from Inter Milan at the beginning of last season, and for City during January.
Gareth Barry was sent off for two bookable offences during the recent Premier League encounter with Liverpool, meaning he missed the FA Cup third-round tie against Manchester United.
It was the early dismissal of Vincent Kompany for a two-footed tackle on Nani during that game that infuriated manager Roberto Mancini.
City failed to overturn the Belgian's four-match suspension, which he will complete on Wednesday.
Mancini then sparked a row by condemning Wayne Rooney's involvement in the dismissal, only to wave an imaginary card himself when Glen Johnson dived in on Lescott during that Carling Cup encounter with Liverpool at the Etihad Stadium.
Steven Gerrard angrily responded to that gesture, which Mancini repeated when Maynor Figueroa deliberately handled to prevent Sergio Aguero racing clear of the Wigan defence at the DW Stadium a week ago.
Now the City manager must face being without a key member of his squad for four crucial games whilst midfielder Yaya Toure is still absent on African Nations Cup duty with the Ivory Coast.
On Sky yesterday, pundit Graeme Souness described Balotelli as "a car crash waiting to happen", indicating the 21-year-old could cost City the title.
Balotelli has been sent off three times in his fledgling City career and was branded "stupid" by Mancini following the second of those, against Dynamo Kiev in the Europa League last season.
However, the City boss was more forgiving when he was dismissed for two debatable yellow cards during a Premier League meeting with Liverpool at Anfield in November.
There have been other off-field incidents that have sometimes even led to City supporters questioning Balotelli's contribution, not least the incident in October when fire crews were called to his house in Cheshire when he attempted to set off fireworks in his bathroom.
