The four-time World Player of the Year and his father, Jorge Messi, are accused of evading 4.2m euros (£3.4m) in tax on his image rights.
They are suspected of setting up companies in Uruguay and Belize to avoid paying tax in Spain.
Both men deny the allegations, which date back to between 2007 and 2009, saying the deals were done by Messi's former agent without their knowledge.
Messi and his father were questioned in a closed session in a court in Gava, the Barcelona neighbourhood in which the footballer has a home.
Friday's hearing was to determine whether or not the court will pursue the case further.
The pair have already paid back 5m euros (£4.2m) to the Spanish state but with the authorities cracking down on tax fraud amid a national financial crisis, this has not prevented the prosecution.
Messi had earlier said: "We have always fulfilled our tax obligations following the advice of our tax consultants who will take care of clarifying this situation."