A statement from the Attorney General's Office confirmed to Press Association Sport that the Madrid Prosecutor's Office had lodged the papers, relating to 2011 and 2012, with the municipal court.
Other stars to have fallen foul of the tax laws include Neymar, Radamel Falcao, Javier Mascherano and Ricardo Carvalho, says the Daily Telegraph.
Manchester United manager Jose Mourinho has been accused of defrauding Spanish authorities of €3.3m (£2.9m, $3.7m) in tax during his time at Real Madrid.
Ronaldo is now on duty for Portugal at the Confederations Cup in Russian Federation which ends on July 2.
The four-time world player of the year, who said last week his "conscience is clear", is threatening to leave Real Madrid over the affair. "Up to this point, neither Hacienda [the tax office] nor the prosecutors have contacted Jose Mourinho or the advisers who were under contract during the [tax] inspection process", Gestifute said in a statement.
Mendes' agency, Gestifute, released a statement saying Mourinho had not received any official notification about the accusations against him.
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The 29-year-old and his father Jorge Horacio Messi were found guilty of using companies in Belize, Britain, Switzerland and Uruguay to avoid paying taxes on 4.16 million euros of Messi's income earned from his image rights from 2007-09.
"The Spanish government in turn, through the tax department, issued a certificate in which it attested that he regularised his position and was in compliance with all his tax obligations".
Earlier this month, Spanish prosecutors filed a criminal tax fraud lawsuit against Cristiano Ronaldo, alleging that the Real Madrid forward defrauded the Spanish state out of €14.7m (£13m) between 2011 and 2014.
When media speculation emerged in December that Mourinho was being investigated by Spain's Tax Office over unpaid taxes, the former Porto, Chelsea and Inter Milan boss denied any wrongdoing and said he "has nothing to hide."
Barcelona's Lionel Messi was convicted of tax fraud previous year and given a 21-month prison sentence, although under Spanish law he did not have to spend time behind bars.
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