They claim that Mourinho, who took over at United a year ago, failed to declare 3.3 million euros ($3.7m, £2.9m) during his time in the Spanish capital - 1.6 million euros in 2011 and 1.7 million euros in 2012.
"The corporate structure was used by the accused in order to make the benefits derived from image rights opaque", the prosecutor said in a statement.
Ronaldo, who is now facing four charges of tax fraud in Spain, was reported to want to leave Real Madrid and Spain.
The 32-year-old has been heavily linked with a return to Manchester United, while Paris Saint-Germain are also believed to have offered the player a huge contract.
The Madrid president, who was re-elected unopposed this week, gave a full-length interview to Onda Cero where he spoke at length about the Ronaldo situation.
It will now be up to a judge to decide whether to take the matter to court.
In this way, Lionel Messi has been found guilty of fraud, and recently Cristiano Ronaldo accused by prosecutors of evading €14.7m.
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Manchester United manager is facing a probe into his tax affairs during his time as Real Madrid boss.
The claims against Mourinho come amid a lengthening list of tax fraud cases involving football stars in Spain. It released a statement saying: "To this date, neither the Spanish tax authorities, nor the public prosecutor has contacted Jose Mourinho or his advisers".
Ronaldo, who played under Mourinho at the Bernabeu, has denied the charges and is threatening to leave Spain.
In three years with Real Madrid, Mourinho won La Liga in 2012 and the Spanish Cup in 2011.
Less than a month after Spain's Supreme Court upheld his 21-month sentence after being convicted of tax fraud, Barcelona star Leo Messi is expected to avoid prison time.
The prosecutor said last Tuesday that there was evidence that Ronaldo used a shell company in the Virgin Islands to hide the money he had made from image rights.
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