The Premier League said on Tuesday that City had used "sham" commercial contracts as part of schemes to inflate revenue and understate costs by more than £900 million ($1.2 billion) over nearly a decade.
Etihad, City's principal sponsor since 2009, said it "categorically rejects any finding, conclusion or implication" that it was involved in improper commercial arrangements.
In a statement, the airline said the league never contacted or consulted it during the commission process and gave it no opportunity to provide information or challenge material that may have reflected adversely on the company.
"Etihad is deeply concerned by the way this matter has been communicated publicly," the statement said. "The lack of clarity and transparency, together with the selective disclosure of information, has created damaging implications for Etihad despite the airline not being named in the published decision."
City have denied any wrongdoing and said they intend to appeal.
A Premier League spokesperson said on Wednesday they would not be commenting on the Etihad statement.
Etihad added that the Premier League's public communication of the findings, following what it described as selective leaks and reporting, had harmed its reputation.
While reaffirming its support for Manchester City and its longstanding partnership with the club, the airline said it was seeking legal advice on the options available to protect its interests.
"We stand with the club, its supporters and our wider Etihad community as Manchester City challenges the commission's conclusions through the processes available to it," the statement said.