A statement from Real said Perez, 73, had returned a positive result during the club's routine testing and was currently asymptomatic.
Perez first became Real chief in 2000 overseeing the signing of world stars such as Zinedine Zidane and David Beckham in what became known as the 'Galactico' era before resigning in 2006.
He returned to Real in 2009 and ushered in a second era of high profile signings including Kaka and Cristiano Ronaldo in the same summer.
The team have won four Champions Leagues in his second spell, adding to their 2002 triumph in his first tenure, while he has also overseen major renovations to the club's Santiago Bernabeu stadium, which began last year.
Perez is also the chairman of the Spanish construction conglomerate ACS and its principal investor, holding 12.5% of the infrastructure giant's capital.
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