The FA said the issue referred to rules concerning "club whereabouts", but no other information was given.
Under FA rules, English clubs are required to provide the correct details of training sessions, as well as player addresses, so that they are available for drug testing at all times.
The BBC reported that information was not updated following a change to training routines.
"Manchester City have been charged in relation to the FA's rules on anti-doping," an FA statement read.
"It is alleged the club failed to ensure that their 'Club Whereabouts' information was accurate.
"City have until 19 January 2017 to respond to the charge."
City are currently fourth in the Premier League, seven points behind leaders Chelsea, and take on Everton at Goodison Park on Sunday.
Pep Guardiola's side won 5-0 at West Ham in the FA Cup third round on Friday.