The Football Association has charged Chelsea with misconduct for carrying out "independent private drug testing on some of its players" last year.
The FA alleges Chelsea breached Rule E25, which forbids private testing.
Chelsea said the charges were directly related to striker Adrian Mutu, who was subsequently sacked for taking cocaine.
The Premiership champions have until 23 September to respond and said they would "vigorously" defend themselves against the charge.
"The club feels that it has done nothing morally wrong," Chelsea said in a statement.
The FA charge relates to 12 July 2004, when Chelsea tested a number of players at pre-season training.
The FA rule says: "The independent private testing/screening of players by clubs, club officials or any other person subject to FA rules is prohibited."
Chelsea said the test the club carried out on Mutu had proved negative.
"Subsequently, the same player failed an FA approved drugs test for cocaine and his contract with Chelsea was terminated," said the club statement.
"During the hearing into this failed test he also admitted to taking this Class A drug on several occasions."
The FA does not allow independent testing in case it leads to incidents where clubs could try to cover up drug use by squad members.
The Chelsea statement continued: "Chelsea is absolutely committed to the fight against drugs in football.
"We believe we have demonstrated this by our actions and would never attempt to contravene any rules in order to cover up drugs in sport.
"We have made it clear publicly that we will adopt a zero tolerance policy to anybody who fails a drug test and rejects the chance of help and rehabilitation when offered by the club."
Chelsea also sacked Australian keeper Mark Bosnich in January 2003 after he tested positive for cocaine.