Jose Mourinho was accused of defrauding Spain of €3.3m (£2.9m; $3.6m) in taxes between 2011 and 2012.
A prosecutor said Mr Mourinho, 54, did not declare income from image rights in order to get an “illicit benefit”.
A statement released on his behalf said he “has not received any notification”.
A spokesman for the Manchester United manager said: “José Mourinho has not received any notification with regards to the news published today. To this date, neither the Spanish tax authorities, nor the public prosecutor have contacted José Mourinho or his advisers who were hired for the inspection process.
“José Mourinho, who lived in Spain from June 2010 until May 2013, paid more than €26m in taxes, with an average tax rate over 41%, and accepted the regularisation proposals made by the Spanish tax authorities in 2015 regarding the years of 2011 and 2012 and entered into a settlement agreement regarding 2013.
“The Spanish government in turn, 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.”
Real Madrid forward Cristiano Ronaldo, who played under Mr Mourinho and shares the same agent, is accused of defrauding tax authorities of €14.7m, by also hiding his income from image rights.
He denies the accusations and is threatening to leave Spain. The Portugal international is set to give evidence in his case on 31 July.
Jose Mourinho has blatantly denied all the acquisitions.