The Santiago Bernabeu side have no intention to harm their relationship with the Liga champions, while they have yet to make a formal bid for Malaga star Isco
Both Madrid and Manchester United are believed to be closely monitoring the 22-year-old's situation at the Camp Nou side amid reports that he's unhappy with his lack of regular first-team action at Barca.
However, Perez has made it clear that Madrid have no intention to put their good relationship with Barca at risk by trying to sign Thiago behind the Catalans' back.
"Thiago is a very good player. I do not know whether Barcelona are willing to sell. I can assure that Madrid will not trigger his buy-out clause, though," the Madrid president told Punto Pelota.
"We will not do anything hostile toward Barcelona. If we were ever to make a move for Thiago, or any other Barcelona player, we will speak to Barca first."
Perez then went on to discuss Madrid's interest in players such as Napoli star Edinson Cavani and Malaga youngster Isco.
"Cavani and Isco are both very good players. It's only normal that a club like Manchester City like Isco. However, we have not talked to him about a potential transfer."
The 26-year-old Cavani has a contract with Napoli until June 2017, while Isco, 21, is under contract with Malaga until 2016.