In a court filing, the judge in charge of the case rejected the request of the public prosecutor to try only the Argentine footballer's father.
The pair were accused in 2013 of defrauding the taxman out of €4.16 million ($4.69 million) in taxes related to Messi's image rights between 2007 and 2009 through the creation of fake companies in Belize and Uruguay.
Both Messi and his father denied wrongdoing and instead pointed the finger at a former agent.
The court decision to push ahead with the case against Messi came just a day after Barcelona's public prosecuter said it would not be pursuing charges against the star footballer.
According to the charge sheet published on Tuesday, Barcelona forward Messi was not aware of the fraud committed by his father, Jorge Horacio, who has managed the footballer's affairs since he was a child.
Four-time world player of the year Messi is the fourth richest sportsman in the world, according to Forbes magazine which estimates he earns $64.7 million a year.
Messi's older brother Matias, 32, was briefly detained in Argentina on Sunday after he was found with a revolver in the glove compartment of his car.