Chelsea intend to contest charges arising from groundsman Sam Bethell's altercation with Manchester United defender Patrice Evra in April.
Evra was among a group of players warming down after United's defeat at Stamford Bridge who were asked to move by groundstaff, sparking a row.
Charges against Bethell were dropped by an independent commission on Monday.
But the Football Association has now charged Chelsea for breaching FA rules in relation to his conduct.
Bethell had been charged with improper conduct and using abusive language aggravated by reference to nationality and or race.
But an independent panel cleared him, ruling that the FA did not have disciplinary jurisdiction over him because Chelsea had failed to tell him that he was subject to FA rules.
606: DEBATENow, the FA has charged Chelsea "for their failure to include the required provisions in his employment contract".
The Stamford Bridge club have also been charged with, "failing to ensure that Bethell conducted himself in an orderly fashion and/or refrained from any one or a combination of racist and/or abusive and/or provocative conduct and/or language".
Chelsea have until 25 September to respond to their charges, but have issued a statement declaring their intention to contest the charges.
"We are surprised and extremely disappointed that the decision to charge the club has been taken nearly five months after the incident," it said.
"The charges will be contested as we understand that no racist language was used and that Sam Bethell was doing no more than trying to defend himself.
"Chelsea FC is deeply committed to stamping out racist behaviour and would never condone it."
Evra, meanwhile, will face an improper conduct charge at a hearing on 2 October.
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