The Blancos president called a press conference to insist that there is no truth in the reports claiming the squad had demanded the exit of their coach in the summer
Marca, a newspaper with close links to the club, had suggested on Thursday that the squad, led by Iker Casillas and Sergio Ramos, had told the supremo to choose between the Portuguese and the players during a meeting on Tuesday.
"I break my rule not to speak to the press about the club's day-by-day business due to the seriousness of the allegations published by Marca," Perez said at a press conference.
"I'm not here to talk about Iker, only to deny the information that has come out this morning. I haven't spoken to Mourinho, I came here of my own accord. They cannot play with an institution like Real Madrid.
"It is absolutely false that the captains said anything negative about the coach. No ultimatum was issued by Casillas or Ramos. The level of responsibility of the captains is incompatible with this information.
"The information published today [Thursday] is a pure lie and it's a serious attack against the club. I have a lot of respect for the press and I always listen to criticism, regardless of whether I think it's fair or not.
"But there are limits that must be respected. This is a serious matter. It is not a typical daily rumour, on who we sign or who we dismiss, It's about ethics."
Iker Casillas and Sergio Ramos released a joint statement after the press conference on Madrid's website, which read: "The two captains of Real Madrid want to communicate the following: That the meeting held on Tuesday with the president and CEO of the club never raised any ultimatum from us regarding the character of our coach.
"As captains of the staff and members of an excellent group of people and professionals, we categorically reject the use of our names and the rest of our squad's in support of information that is entirely false.
"We want to show our support for the character of our coach, Jose Mourinho, to whom we owe the greatest respect.
"Finally, we wish to convey to the members and fans of Real Madrid our unalterable conviction that only through the unity of everyone at Real Madrid will we overcome all the challenges that we face each season."
Mourinho already voiced his dismay with the way he has been treated in the press earlier this week, claiming that people are trying to create controversies that do not exist.
Despite Perez's denial, Marca have stood by their story.