The English champions have accepted the punishment, which relates to rule infringements over the past two seasons, the league has confirmed.
This issue is unconnected to the 115 charges City are facing for alleged breaches of the Premier League's financial regulations.
A Premier League statement said: "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 restart obligations."
City have been punished on a sliding scale for each offence.
Their first, a delay of one minute and 18 seconds to the start of the second half against Crystal Palace in August 2022, led to a warning.
But fines ranging from £10,000 to £200,000 have been imposed for each subsequent breach.
The longest delay was two minutes and 46 seconds for the start of the final game of the season against West Ham last season, when City clinched a record fourth successive English title.
The statement added: "Rules relating to kick-offs and restarts 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."
City have not commented directly but the ruling said: "The club has apologised for the accepted breaches... and confirmed that it has reminded the club's players and football management teams of their responsibilities in complying with Rule L.33."
