The prosecutor argued in June that Messi's father Jorge was responsible for the family's finances and not the four-times World Player of the Year.
However, the court in Barcelona has decided that Lionel Messi could have known about and approved the creation of a web of shell companies that were allegedly used to evade taxes due on income from image rights.
The judge in the case ruled that the case against both Messis should continue, according to a statement published on Monday.
Messi and his father were accused last year of defrauding the Spanish state of more than 4 million euros (£3.18 million) by filing false returns for the years 2006 to 2009. They have denied wrongdoing.
One of the world's highest-paid athletes, Messi earns just over $40 million a season in salary and bonuses, according to Forbes magazine, as well as about $23 million from sponsors.
The magazine has him as the fourth top-earning athlete behind boxer Floyd Mayweather, Real Madrid footballer Cristiano Ronaldo and basketball player LeBron James.
(Reporting by Inmaculada Sanz, writing by Iain Rogers, editing by Tony Goodson)
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