The Argentine and his father have paid around 5 million euros to authorities in Spain, but a judge revealed Monday that the charges haven't been dropped.
The Argentine has already appeared in court to answer claims of alleged tax evasion to the tune of 4.1 million euros from 2006 to 2009 and has long declared his innocence.
Nevertheless, the player and his father Jorge Messi paid just over 5 million euros to authorities last year and it had looked as if the case would be closed.
But the judge in Gava, a seaside town just outside Barcelona where Messi owns a property, has decided to proceed with the case against the four-time Ballon d'Or winner and his father.
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Messi has claimed he left all of his business interests to his father and his management team. "Lionel A. Messi was not involved in the decision-making on the management and channelling of his income and did not really know the scope, size, purpose or effects of the corporate network," said a statement for the prosecution earlier this year.
But a new written statement by the judge said Monday that "there is sufficient evidence" that Messi "could have known about and consented to the creation and maintaining of a fictitious financial structure."
The judge also added that because the player's signature is on all of the documents being investigated, the 26-year-old "could have warned about the intervention of others in these cases or read some of these contracts, even if it was only the headers."
It is alleged that Messi's image rights were sold by Jorge — who assumed full responsibility when the case began — using companies in countries like Belize and Uruguay to avoid Spanish tax obligations.