City are reported to have been found guilty of the vast majority of 115 financial misconduct charges brought against them by the Premier League.
They have strenuously denied the charges and City chairman Khaldoon Al Mubarak on Saturday said he is still confident of proving the club's innocence.
City are expected to appeal against their eventual punishment, which is yet to be announced and could include a points deduction, expulsion from the Premier League or a huge fine.
There have also been calls for City to be stripped of their eight Premier League titles won since 2008.
Manchester City Verdict
The Premier League have confirmed that Manchester City have been found guilty of all charges related to breaching financial rules.
The charges relate to breaches between the 2008/09 and 2017/18 seasons, with the club found guilty of breaching the Premier League's financial rules.
An independent commission found that the club had artificially inflated their revenues and reduced costs by more than £900 million during the time period mentioned.
The ruling also states that Manchester City committed multiple breaches of its duties of co-operation and utmost good faith towards the Premier League, and that they were in 'significant breach' of both the Premier League and UEFA's spending limits.
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Rooney's former United team-mates Rio Ferdinand and David de Gea have said their old club should be awarded retrospective title wins.
Rooney, a five-time title winner, was a member of the United side that finished as runners-up in 2012 after Sergio Aguero's dramatic late winner for City against QPR on the final day of the season.
But the ex-England striker does not believe United or any other team should be willing to accept medals after ending in second place.
"I wouldn't feel comfortable about accepting another Premier League medal if I'm being honest, because I don't think we deserve it. We didn't do enough that season to win the league," Rooney told the "Stick to United" podcast on Tuesday.
"I'm thinking as their players, they're there doing everything they can to win the Premier League title and in their minds they've done it."
Rooney admitted he would be heartbroken if any of United's medals were ever taken away from him for something over which he had no control.
"If that happened to me, if all of a sudden Manchester United had been doing the same and my Premier League medal had been taken away, I would be absolutely devastated," the 40-year-old said.
"It might happen, they might take them away, but I wouldn't want it because I don't think as a team we deserved it that year because obviously we didn't finish first.
"So when I see ex-team-mates and other people saying 'I want a medal'. I'm happy with the five I've won. I wouldn't want this one, just 15 years later you get a medal because City cheated.
"Should they get it stripped for what the owners have done? Yeah, maybe, but I wouldn't feel comfortable accepting it."