A lack of success against the Portuguese is the reason behind the pair's comments, according to the Santiago Bernabeu chief
Iniesta accused the freshly appointed Chelsea boss of damaging La Liga during his time at Madrid, while Xavi slammed Mourinho's negative approach.
The Portuguese hit back at Iniesta on Monday when he stated that the midfielder's comments came out of frustration that he ended Barcelona's dominance and Perez has now backed his former coach, too.
"I understand that Xavi and Iniesta are frustrated with Mourinho. They did not win a single one of their last five games against us," the Madrid president told Marca.
"It's not the best of strategies to start criticising your opponent when you cannot beat him.
"Barcelona used to win all the games against Madrid, but then Mourinho arrived at the club. So Jose is right with his comments."
Mourinho won one Liga title, one Copa del Rey and the Spanish Supercopa during his three-year spell at Madrid.