The alleged offences relate to the claims from the West Ham striker Carlton Cole and the Millwall forward Jason Price that they suffered racial abuse from rival fans during the evening tie, which West Ham won 3-1 following extra-time.

Millwall had the charge thrown out on appeal.

A statement from the governing body said: "The FA have issued charges against both West Ham United FC and Millwall FC following the serious crowd disturbances in and around Upton Park on 25 August 2009.

"West Ham United FC have been charged on four counts of failing to control their supporters whilst Millwall FC have been charged on three counts following events at the Carling Cup fixture. It is alleged that both clubs failed to ensure that their supporters conducted themselves in an orderly fashion."

Beyond the alleged racist abuse offences the charges each club will have to answer are "failure to ensure their supporters refrained from violent, threatening, obscene and provocative behaviour" and "failure to ensure their supporters didn't throw missiles, harmful or dangerous objects on to the pitch".

West Ham have received an additional charge of "failure to ensure their supporters didn't enter the field of play" after the pitch was invaded three times by their fans during the game.

The trouble had broken out at around 6pm, before the unrest continued close to and inside the stadium, while during the match, supporters threw missiles at each other.

The FA added that it "has liaised closely with all relevant authorities including the Metropolitan police during the course of its investigations and has been in constant dialogue with both clubs during this time. Both clubs now have a period of 14 days to respond to the charges."

West Ham are expected to fight the charges. They may examine the scenes at the end of the Manchester derby eight days ago, when a Manchester United fan invaded the pitch and appeared to be hit by City's Craig Bellamy, and Carlos Tevez seemed to have a missile aimed at him.

Millwall, meanwhile, will make an official comment regarding how they will answer the alleged offences this morning but it seems likely they will contest the charges. Both clubs may also point out that they feel they complied with all police and safety requests.

Following the incident the sports minister, Gerry Sutcliffe, described the scenes as "a disgrace to football" before backing the FA's call for life bans for those found to have been involved. Andy Williamson, the chief operating officer at the Football League under whose jurisdiction the game fell, said: "We utterly deplore the violence that took place in last night's match. Such behaviour has no place within the game. We will work with the relevant authorities to ensure those behind it are held to account."sons.