Javier Tebas expressed his concerns over the spending of PSG and City at the SoccerEx convention in Manchester on Wednesday.
La Liga lodged an official complaint to UEFA on August 22, calling for an investigation into both clubs for "violation of financial fair play regulations".
A statement for City read: "We note the public comments made by Mr. Tebas today and earlier this week.
"UEFA's statement of the 4th of September is clear and based on accurate information. By contrast, Mr. Tebas' statements are ill-informed and in parts pure fiction.
"As you would expect, Manchester City Football Club and the City Football Group are seeking appropriate legal counsel and will act accordingly on that advice."
"Manchester City with all this oil [money] will take all these players and we need to protect ourselves. These past few years Manchester City have paid out nearly a thousand million on players, PSG £950m."