Earlier this year, the city initiated legal action against the associated party transaction (APT) rules, arguing that they were anti-competitive.
The APT rules are designed to ensure commercial deals with entities linked to a club's owners reflect fair market value.
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The case is separate from an ongoing hearing involving City, with the club fighting 115 charges relating to alleged breaches of Premier League financial rules.
The Premier League said on Monday that City were "unsuccessful in the majority of (their) challenge" and that the tribunal considering the case had determined the APT rules were necessary and pursued a legitimate objective.
But City released a statement saying the tribunal had declared the APT rules "unlawful" and that the league had abused a dominant position under competition law.
The Premier League said the tribunal had supported the legitimacy of the regulations and said it had found them essential to make the profitability and sustainability rules (PSR) effective.
It said the tribunal had agreed with the Premier League that if a transaction was evidently not at fair market value, that would distort competition within the league.
The league also said the panel had rejected City's argument that the purpose of the rules was to discriminate against clubs with ownership from the Gulf region.
The Premier League said the panel found in favour of City in "two respects only" -- that shareholder loans should not be excluded from APT rules and that a "limited number of amendments" to the APT rules made earlier should not be retained.
Manchester City said the panel found the APT rules were "structurally unfair" and that the panel had set aside specific decisions of the Premier League to restate the fair market value of two transactions entered into by the club.
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