The pair are alleged to have filed incorrect tax returns between 2006 and 2009 and a court located near Barcelona confirmed on Wednesday that a payment of just over € 5million has been received.
This means Messi will not be set bail, as the State Agency for Tax Administration had requested, with the statement to the media explaining that "given the global impact" of the Barcelona and Argentina star, there was no doubt as to his "solvency".
The statement added that the payment meant there was little chance of Messi and his father withholding further monies "during the legal process of a pending tax fraud trial".
A court hearing has been set for September 17, although Messi's lawyers have requested this be postponed due to prior commitments.
Spanish authorities have looked to crack down on tax payments in recent years. Former Barcelona and Real Madrid star Luis Figo was ordered to pay €2.4m in missing tax payments last year.
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