Real Madrid director Jorge Valdano has been sacked by the club, a move which hands full control of transfers over to manager Jose Mourinho.
"We have decided to end the contractual relationship with Jorge Valdano," Perez said at a news conference at Real's Bernabeu stadium following a meeting of the club's board of directors.
"I want to stress how painful the departure of Jorge Valdano is to me. We have traveled a long distance together. Mourinho did not make any demands. He asked for more autonomy in line with how English clubs are organised. Everything that we do we do because they are the right decisions that do not take into account personal sentiment.
''The experience of the season just ended has shown the need for new organisation at the club, giving autonomy to our coach. This is the first step in our reorganisation process which we will develop in the coming weeks.''
Valdano and Mourinho had clashed earlier this season with the Portuguese boss outlining his desire to spend money on another striker during the winter transfer window after Gonzalo Higuain was ruled out of action for four months.
Mourinho was angry that Valdano had spoken to the press after Real Madrid's shock 1-1 draw against bottom club Almeria in January, claiming 40 million striker Karim Benzema was suffering "a great injustice" by being left out of the side.
Valdano had said: ''We are spectators to whatever the coach decides. I hope Benzema does not stay on the bench for too long. The situation surrounding him is unfair.''
But Mourinho hit back: '' 'I pick the team, and if I need any help then I have my coaching staff. I did not speak about it again. I am not the one sending messages. I got where I am thinking with my own head and I am too old for messages in the newspapers. Little messages don't get to me."
Eventually loan signing Emmanuel Adebayor arrived from Manchester City but Valdano admitted that he may have to step away from his post for the good of the club.
"If I have to step away for Mourinho to feel more comfortable, so be it," he said. "From my responsibility, it is important not to create more tension here. The coach feels more comfortable in his relationship with the president, so we must seek working conditions that are comfortable. The enemies are the enemies and that is where efforts should be focused."
Perez has now taken action to remove the tension between the two and reports suggest that Valdano's payoff is in the region of €3.5 million.
Valdano himself said: ''I have always respected Real Madrid. I've never turned the club into a battlefield. I always put my position as director general before who I am, and I have always avoided fighting that battle.
''I have great respect and love for this club, and all my efforts were aimed at living up to the greatness of this team.
''I believe Jose Mourinho staying on is good for a club that's been unstable in the past. It needs to settle for a reasonable period of time. He's done a good job, I believe he is a good coach and I find it normal that he stays on.
''Real Madrid is great, which doesn't mean this new structure belittles it. The president came up with this solution to resolve a difficult situation that wasn't easy to manage.
''It is always painful to leave people and places you love. The public had to know about this and I wished to say goodbye.''