Masters was speaking publicly about City's ongoing case of more than 100 alleged breaches of the league's financial rules on Tuesday.
Recently, Everton and Nottingham Forest were accused of breaking the rules. Everton also received a points penalty earlier in the season.
On Tuesday, Masters was asked why the cases against Nottingham and Everton passed through the system faster than those against City.
The two clubs mentioned first are accused of much fewer rule violations than the league champions.
– I understand the question, but they are two completely different things. “Whichever club broke the rules is in the same position as Nottingham and Everton,” Masters said.
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– It should be dealt with on a completely different level
He later confirmed that a hearing had been scheduled in the case against Manchester City.
The size and content of the accusations against City mean that they must be dealt with on a completely different level. A date has been set for the hearing, but I cannot say when.
The Manchester club is accused of committing more than 80 violations of the league's financial regulations, in addition to 30 other alleged violations due to their unwillingness to help cooperate with the investigation.
These charges were announced in February of last year.
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If found guilty, they could face a points deduction or even expulsion from the league.
Everton conceded the biggest penalty in league history earlier this season. The Merseyside club received a ten-point deduction after violating the rules of financial fair play in the league. This ruling has been appealed.
The number of allegations and the scale of Manchester City's alleged abuses means that any potential punishment the club faces is likely to be far more severe.
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