The judge handling the case at Barcelona Provincial High Court overruled the prosecutor and turned down a request from Messi's lawyers that he should avoid trial as his father took control of his financial affairs.
Read more: Prosecutors drop charges against Messi
Both Messi and his father Jorge Horacio Messi have been ordered to appear in court on charges of defrauding Spanish authorities of £3m of the player's image rights earnings through shell companies set up by his father in Uruguay, Belize and Switzerland between 2007 and 2009.
The pair deny any wrongdoing.
Lawyers acting on behalf of Spanish tax authorities have recommended 22-month jail sentences for both defendants and fines of more than £1.5m for Jorge Messi.
According to AFP, the judge wrote in a court filing that "there are rational signs that the criminality was committed by both accused parties".