Last week Xavi criticised the Portuguese coach's style of football and declared he "has left no legacy for the future", while Iniesta said the new Chelsea boss had "damaged Spanish football" due to his confrontational style.
In his three years at Madrid Mourinho was the main antagonist in the rivalry between the two biggest clubs in Spain, most famously poking then Barcelona assistant coach Tito Vilanova in the eye after a match in August 2011.
Mourinho won Madrid's first league title for four years in 2012 and although Los Blancos lost out on the trophy to the Catalans last season, they overcame Vilanova's side in the Copa del Rey, the Spanish Super Cup and in their last league fixture.
The former Inter boss hit out at Iniesta during his unveiling at Stamford Bridge yesterday, saying: "I damaged Spanish football by being the coach who broke Barcelona's dominance."
And Perez, speaking during an interview with Marca TV, concurred with the 50-year-old's assertion.
"I understand why Xavi and Iniesta are angry with Mourinho, they haven't beaten us in any of the last five games," he said.
"It's not a good strategy to criticise your opponent when you don't win."
Referring to Mourinho's comments, Perez then added: "Mourinho ended Barca's period of always beating Madrid, he was right when he said that."
Mourinho won three trophies in total during his tenure at the Bernabeu while Barca won seven in the same period and Catalan midfielder Cesc Fabregas was quick to laugh off the former Porto manager's comments.
"Madrid ended our hegemony?" he told radio station Onda Cero. "We have just won the league by 15 points."
Real have been heavily linked with a move for Gareth Bale this summer and Perez, while admitting that Madrid would be keen on signing the Tottenham forward, revealed they were not in the process of bidding for him just yet.
"This club always wants to sign the best players and we have a good relationship with Tottenham," he said. "But first we must see who our coach is going to be and from then on we will go about planning our next squad."
One man being linked with a possible move away from the Spanish capital is Cristiano Ronaldo.
The Portuguese forward's contract expires in 2015 and speculation has mounted over a possible move back to former club Manchester United.
But Perez has dismissed that talk and believes that Ronaldo will finish his career in Madrid.
"Cristiano will end up retiring in Madrid," he said. "It's his natural place."