An audit from State Comptroller Thomas DiNapoli's office claims the MTA gave Apple an unfair edge when the company bid for its Grand Central Terminal store location last year.
The report says the agency worked exclusively with Apple for more than a year before issuing a request for proposals.
The audit also found the tech company bought out the restaurant that previously occupied the space for $5 million.
That amount became the required upfront payment for the proposal process.
In a statement, the MTA says the audit is "not fact-based" and that the lease process was both open and transparent.