Barton, 29, accepted a charge of violent conduct toward Sergio Aguero following his red card at the Etihad Stadium for an elbow on Carlos Tevez, which was his second sending-off of the season.
But he has denied a second charge of violent conduct which relates to his apparent attempt to headbutt City captain Vincent Kompany.
The player has requested a personal hearing, the date of which has yet to be set, while QPR will be holding their own inquiry into what happened.
A club statement said: "Queens Park Rangers Football Club can confirm that a full investigation in relation to Joey Barton's dismissal and subsequent events against Manchester City on Sunday will be carried out following the conclusion of his FA hearing.
"The club will be making no further comment at this stage."