The Premier League released a statement to reveal the champions had made the breach relating to “kick-off and re-start obligations.”
Over the period of two seasons, City raked up fines of just over £2.09m for delaying kick-off or the restart after half-time.
Sometimes, the delay was as short as 79 seconds but still cost £100,000.
A statement read: “The Premier League and Manchester City FC have entered into a sanction agreement after the club accepted it had breached Premier League Rule L.33 relating to kick-off and re-start obligations.
“The breaches relate to a number of Premier League matches during the 2022/23 and 2023/24 seasons.
“Rules relating to kick-offs and re-starts help ensure the organisation of the competition is set at the highest possible professional standard and provides certainty to fans and participating clubs.
“It also ensures the broadcast of all 380 League matches around the world is kept to schedule.
“As required by the Premier League Rules, the sanction agreement has been ratified by three members of the Independent Judicial Panel.”
City are due for a hearing into the 115 Premier League charges they have been hit with for alleged financial irregularities.
The club are accused of breaching regulations from the 2009-10 season onwards.
Chief among the alleged violations are allegations of over financial reporting and a refusal to cooperate with the Prem’s investigation.
City have vehemently denied any wrongdoing.
The case is heading to a hearing in November – 18 months after the charges were originally brought – and will be heard by an independent panel over a six-week period.