The 32-year-old was livid over being singled out for disproportionate treatment after prosecutors accused him of defrauding the authorities of €14.7 million (£12.8 million).
The pair fell out during Mourinho's final season at the Bernabeu but they are both on Mendes' books.
Perez first became Real president in 2000, seeing off incumbent Lorenzo Sanz by promising to lure winger Luis Figo from bitter rivals Barcelona, which he quickly delivered on by bringing the Portuguese worldwide to the Spanish capital for a then world record fee of 62 million euros.
Perez assured fans that the forward would be honouring his contract with Real Madrid, but revealed that he would not discuss the former Manchester United player's future until after Portugal had finished their Confederations Cup campaign. Madrid may well get another five years of elite football out of him.
Spanish daily AS have an interesting article on Monday looking at clubs who will profit if Cristiano Ronaldo leaves Real Madrid this summer.
Does he want to move back to Manchester United or is his preference Paris St-Germain?
"Even though he would make more of an impact at other teams that don't have such an impressive commercial appeal".
Madrid, though, will do everything they can to keep Ronaldo.
If Wayne Rooney leaves the club, the team would be without a real talisman, and Rooney has been on the decline for a while now.
And the United chief is willing to bury the hatchet to bring in Ronaldo's goals and personality. "Definitely United will be in a position to afford this deal". United would do well to avoid the Ronaldo-shaped distraction and remain focused on key targets that were sought long before this saga came to light.