The Argentine international and his father Jorge were accused last year of not paying tax on earnings from the player's image rights from 2007-2009.
Both Messi and his father denied wrongdoing and instead pointed the finger at a former agent.
But prosecutors in Barcelona on Wednesday decided to press ahead with the case.
"While it is understandable that a player of this magnitude is not aware of all the details of managing a millionaire," they said "there are elements of a fiscal debt".
Messi and his father have been accused of using companies in Belize and Uruguay to sell the player's rights -- an allegation the player denies.
Jorge has since admitted that his son knew nothing of the alleged fraud, but the appeals court rejected the defence.
"Messi could have had knowledge of the irregularities of contracts which he was signing," said a statement.
Four-time World Player of the Year Messi is one of the world's richest sportsmen.
Forbes magazine estimated that in 2014 his income was $64.7 million (€47.30 million)