The contract includes naming rights for Eastlands, a major input into a yet-to-be-built training facility close to the stadium and an extension of their shirt sponsorship.
As Etihad are an airline based in Abu Dhabi, home of Blues owner Sheikh Mansour, concerns have been aired that the deal has been artificially inflated to help City achieve UEFA's demand to live within their means as part of their financial fair play initiative.
Arsenal manager Arsene Wenger earlier this week claimed the deal "raises the real question about the credibility of Financial Fair Play", and Ayre has now added his voice to the chorus of disapproval.
Quoted by The Independent on the club's pre-season tour of Asia, he said: "Is Etihad, Manchester City and Sheikh Mansour a related party? If they are, then it's up to UEFA to rule on them.
"When I spoke at Soccerex earlier this year, I was on a panel about financial fair play. The guys from UEFA who are managing it said there would be a robust and proper process about related-party transactions."
Of the stadium name change, he added: "It hasn't happened anywhere in Europe where a football club has renamed its existing stadium and it's had real value.
"It was called the City of Manchester Stadium or Eastlands for the last nine years and now it's going to be called something else - and someone has attached a huge amount of value to that.
"I find that odd because there is no benchmark in football that says you can rename your stadium and generate that amount of value. Mike Ashley tried it at Newcastle [sportsdirect.com@St James' Park]. But nobody calls it that and it doesn't have that kind of value."
City on Tuesday night issued a statement branding Wenger's comments "unfounded and regrettable".
The statement added: "Manchester City is a pro-active member of the European Clubs Association and is working actively and with transparency with regard to financial fair play."