Clubs are required to provide accurate details of training sessions and player whereabouts so that they are available for testing at all times.
The club allegedly failed to ensure that their 'club whereabouts' information was accurate.
City have until 19 January to respond to the charge.
It is understood the information was not updated following a change to training routines.
Manchester City have been charged by the Football Association for failing to ensure anti-doping officials knew where players were for drugs testing.