Mourinho has continued to attract headlines in Spain for his conduct in and away from the dug-out and was widely criticised for jabbing a finger in the eye of Barcelona assistant Tito Vilanova during the Spanish Super Cup last month.
Several Madrid members spoke this morning of their unease at having the Portuguese in charge and expressed their concern that his antics were damaging the club's reputation worldwide, but Perez was unequivocal in his backing.
"We believe in this team and in the best coach in the world: Jose Mourinho," he said.
"He understands what it means to be Real Madrid's coach and he has a high level of empathy and compromise with the club.
"His 'Madridismo' is unquestionable. We should remember the team wasn't even a top seed in the Champions League when this new era at the club began two years ago.
"Last season we reached the semi-finals, something that hadn't happened since the 2002/03 campaign.
"We took more points than any other side in the group stage, and were the top scoring and least scored upon team."
Mourinho was recently handed more power at the Bernabeu after Mourinho won a power struggle with now-departed sporting director Jorge Valdano.
Perez added: "The experience of last season proved we needed a new and modern organisational structure at the club that would give our coach autonomy and avoid dysfunction due to the existence of a sports director general's office."
The general assembly also approved plans to redevelop the Bernabeu with a new roof, a new facade and better car parking facilities.
"The stadium must be subjected to constant evolution and must become a symbol for state-of-the-art facilities and excellence," Perez said.
"We want to transform it and make it a leading example for modernity, for sports, for Madridismo and for the city of Madrid. We want it to be a building whose singularity, quality and beauty goes beyond our borders.
"We want to provide it with an enveloping skin that will serve to roof all seats so that our supporters won't suffer from adverse weather conditions while watching a game."