The Spanish club has made it clear that the defender is not for sale, while also revealing that Jose Mourinho could have stayed put had he won silverware this term.
The 30-year-old lost his starting berth at Madrid to Raphael Varane this season, leading to speculation that he could push for a move away from the Santiago Bernabeu side in order to get regular first-team action elsewhere.
Nevertheless, Perez has made it clear that Madrid aims to keep the center back - who has a contract until 2016 - on board for the foreseeable future.
"Pepe is not for sale. He is going nowhere this summer," the Madrid president told Onda Cero.
Perez then went on to reflect on Jose Mourinho's departure and stated that the Portuguese coach would probably have stayed put had the club won the Champions League, while adding that he sees Carlo Ancelotti as the ideal replacement.
"If we had won the Champions League and the Copa del Rey, Mourinho would probably have stayed put," he added.
"Ancelotti? He would fit in very well at Madrid. He is a good people manager and a great coach."
The current Paris Saint-Germain coach remains the Blancos' only option for the vacant position of head coach for now as the team is hopeful that PSG will eventually let go of the Italian.