Chelsea chief executive Peter Kenyon says Uefa has made an "unprecedented attack" on the Stamford Bridge club.
Kenyon rejected claims Chelsea lied about Frank Rijkaard meeting referee Anders Frisk at half-time during their Champions League tie in Barcelona.
He says Uefa has inflamed the situation by calling Jose Mourinho, Steve Clarke and security officer Les Miles "liars".
He said: "These statements called into question the integrity of the club and we cannot let them stand unchallenged."
Uefa charged Mourinho, Clarke and Miles with bringing the game into disrepute for making "false declarations" in a report which alleged Rijkaard visited Frisk's dressing room at the Nou Camp.
Mourinho is also charged with failing to appear at the post-match news conference and the club are also up for the team's late arrival on to the pitch for the second half.
These charges will all be looked into on 31 March.
Kenyon added: "Chelsea are both surprised and disappointed that at least one individual within Uefa appears to have launched an unprecedented attack on the club.
CHELSEA IN THE DOCK
Uefa investigates two charges from first game at Barcelona
Probable outcome: Fine
Uefa hearing into Chelsea's claim about Rijkaard and Frisk
Possible outcome: Mourinho touchline ban
"Chelsea fully adheres to, and respects, the processes of Uefa and is under no illusion about the seriousness of these charges.
"However, the statements against Chelsea, Jose Mourinho, Steve Clarke, and Les Miles by at least one senior Uefa official means we are no longer able to keep our own counsel.
"Unfortunately some within Uefa have decided to ignore their own organisation's reputation for fairness and correct procedure by playing out this debate in the public arena ahead of any hearing.
"The use of such language, and the nature of the public statements as a whole, give us grave concern about our chances of receiving an impartial and fair hearing.
"Our defence has been dismissed before it has even been considered. Our witnesses have been branded as liars without any opportunity to be heard or defend themselves.
"That offends all principles of justice both in England and across Europe."
The Blues face Bayern Munich in the Champions League quarter-finals but the fall-out from the two ties against Barca refuses to die down.
Referee Frisk retired from football after receiving death threats, although Uefa cleared Mourinho of being responsible for stoking that atmosphere.
Even after the second leg Uefa was forced to investigate after Barca striker Samuel Eto'o claimed he was racially abused by a Chelsea steward, which the Blues denied.