The accusation against Mourinho comes a week after the Madrid-based prosecutor's office accused Real Madrid forward Cristiano Ronaldo of defrauding Spain's tax office of 14.7 million euros ($16.5 million).
The allegations against the Portuguese amount to a sum of £2.9 million (€3.3m), according to Spanish publication El Pais.
Mourinho joined Real Madrid football club in March 2010, transferring his residence for tax purposes to the Spanish capital after a spell as manager at Inter Milan.
Prosecutors said he had failed to declare revenues from his image rights in his Spanish income tax declarations from 2011 and 2012, "with the aim of obtaining illicit profits".
The prosecutor said Ronaldo used shell company in the Virgin Islands to cheat on his taxes.
Mourinho is gearing up for a bust summer in the transfer market as he tries to build a squad capable of competing for major honours next season and United have already snapped-up centre-back Vcitor Lindelof from Benfica.
The Portuguese coach has become the latest high-profile football figure accused of tax fraud.
A request for comment from Mendes' agency, Gestifute, was not immediately answered.