"(Valencia president) Manuel Llorente is clear about what he has to do and so am I. The operation is a question of time," Perez told television station Canal Nou.
"We have the whole summer in front of us and it will be important to explain the signing very well to both sets of fans."
Perez has already spent around 68 million euros to land Brazil playmaker Kaka from AC Milan and has had an 80 million pounds offer accepted for Manchester United's Portugal winger Cristiano Ronaldo.
Negotiations for Spanish international Villa's transfer to Real ran into problems last weekend, with differences over his value the main sticking point according to media reports.
"Kaka and Cristiano Ronaldo are two strategic pillars of this project," said Perez.
"These are players that have won the Ballon d'Or and FIFA world player of the year, who I describe as 'investment' players because they have an international reach which others maybe haven't reached."
Financially-troubled Valencia have debts of more than 450 million euros, according to media reports.
Spanish sports daily Marca said last week a deal was in place under which Real would sign Villa for around 37 million euros, with striker Alvaro Negredo moving in the opposite direction to Valencia.
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