The chairman and chief investigatory, Yves Leterme, the former prime minister of Belgium, is now considering whether he agrees with that view, that City do have a case to answer.
The investigatory chamber of UEFA's Club Financial Control Body launched formal proceedings in March.
The Etihad dwellers are claiming innocence despite series of damaging revelations published by German outlet Der Speigel.
City were successful in their pursuit of a second successive Premier League title on Sunday, beating Brighton and Hove Albion 4-1 to finish one point ahead of second-placed Liverpool, who defeated Wolverhampton Wanderers 2-0 at Anfield.
Manchester City have said they are "fully cooperating in good faith" and have provided "comprehensive proof" that accusations of financial fair play (FFP) irregularities are false.
The latest online version of the New York Times article does not contain any reference to "people familiar with the case".
The club have been under investigation by Federation Internationale de Football Association, the Premier League, the FA and UEFA since March, as allegations that the club have breached FFP regulations in their pursuit of dominance reach fever pitch.
If found guilty, City could be excluded from European competition but no timescale regarding the investigation has been made public and the club are angered by reports UEFA investigators will recommend a ban.
Following the end of a colossal bid for the Premier League title, the Reds' sights can now be trained on the task of overcoming Tottenham Hotspur in Madrid.
City were fined 60 million euros ($67.3 million) and subjected to squad, wage and spending caps in a 2014 settlement agreed with UEFA following a previous breach of the rules.
Manchester City's title winners have been filmed mocking Liverpool by appearing to sing a vile song referring to Jurgen Klopp's side as "victims" and their fans being "battered on the streets".