Prosecutors claim that the 54-year-old manager failed to declare income of €1.6 million in 2011 and €1.7 million in 2012, "with the aim of obtaining illicit profits".
The 32-year-old Portuguese star is facing four charges of fraud through offshore companies between 2011 and 2014 and will appear before a judge on July 31, judicial sources told AFP.
However, player nor club has denied rumours of an exit after eight years at Real Madrid.
A statement from the Attorney General's Office confirmed that the Madrid Prosecutor's Office had lodged the papers, relating to 2011 and 2012, with the municipal court. 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 Spanish government. through the tax department, issued a certificate in which it attested that he had regularised his position and was in compliance with all his tax obligations", Gestifute said.More news: US Attorney General Sessions hires private attorney
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The Red Devils are preparing for a return to the Champions League next season after winning the Europa League last term.
Last year, Barcelona forward Lionel Messi and his father Jorge were found guilty of tax evasion on the Argentina international's image rights, with more than €4m owed in back payments.
But club president Florentino Perez insisted that Ronaldo will be staying at the Spanish giants and no offer has been received. "That's why I will speak with him when he gets back and see what's up", Perez told Spanish radio Onda Cero late Monday.
There have been suggestions that Ronaldo is using links to both United and Paris Saint-Germain to earn a new contract at Real Madrid or in hope of stopping or quietening allegations of tax avoidance against him.
Cristiano Ronaldo has been calmed down by Florentino Perez's public backing of him and no longer wants to quit Real Madrid, according to reports in Spain.
Solhekol tweeted: "Real Madrid president Perez says they have not received any offers for their players this summer".