The Premier League side were charged by the FA last month for failing to keep their 'club whereabouts' information accurate for the purposes of drugs tests.
Under the FA's rules, clubs are duty bound to keep records of training dates, the start and end times of sessions, where the sessions take place and the overnight addresses of their players.
The FA said in a statement released on Thursday: "Following an Independent Regulatory Commission hearing, Manchester City have been fined £35,000 and warned as to their future conduct after admitting a breach of the FA's rules on anti-doping.
"City were charged with failing to ensure their 'Club Whereabouts' information was accurate, contrary to Regulation 14(d)."
That regulation specifies: "It shall also be a breach of this regulation 14 by the club if the information contained in such reports is either initially inaccurate or has not been updated by the club as necessary to ensure it remains accurate."
It is understood that the problem arose due to administrative errors on City's part.