The Manchester United boss is accused of £2.91million (€3.3m) worth of tax fraud committed in 2011 and 2012.
Mourinho, who is yet to comment, is among a host of big names who have become embroiled in tax scandals in Spain.
Mourinho was Real Madrid coach from 2010-13.
Real Madrid president Florentino Perez says that he is ready to offer manager Zinedine Zidane a new contract "until whenever he wants".
The prosecutors claim that the sums were missing from Mourinho's tax returns in the respective years with the intention of "deriving unlawful benefit".
They claim that Mourinho, who took over at United previous year, failed to declare € 3.3 million (Rs 23 crore approx.) during his time in the Spanish capital - € 1.6 million in 2011 and € 1.7 million in 2012. But Spanish prosecutors stated the Real Madrid star used a shell company to hide incomes made from image rights.
"To this date, neither the Spanish tax authorities, nor the public prosecutor have contacted Jose Mourinho or his advisers who were hired for the inspection process", the statement said.
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Mourinho also reveals that he paid "more than 26 million euros in tax" and "entered into a settlement agreement regarding 2013". They also said they signed another related statement for 2013.
The news also "comes immediately after it was announced that Cristiano Ronaldo will testify in his own tax fraud case next month", adds the paper.
The statement said that the Spanish government, through tax authorities, "issued a certificate in which it attested that he had regularized his position and was in compliance with all his tax obligations".
Real Madrid turned down the opportunity to sign goalkeeper David de Gea from Manchester United last summer, club president Florentino Perez said today while playing down the possibility of bidding for the Spain global again. Ronaldo has denied the charges.
Just weeks after Leo Messi was sentenced for tax fraud and just days after Cristiano Ronaldo threatened to quit Spain over being accused of owing €14.7m in tax, Mourinho is the latest to be accused.
Adriana Garcia is a Valencia-based football writer who covers La Liga for ESPN FC.
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