“We learned about the action begun by the Spanish prosecutor through the media,” Messi wrote in a statement on his official Facebook page.
“It is something that surprises us because we have never committed any offence,” the statement added.
“We have always fulfilled all our tax obligations following the advice of our tax consultants, who will take care of clarifying this situation.”
Messi, who will be 26 this month, is one of the world's highest-paid athletes with a salary of just over $20 million a season, according to Forbes magazine.
On top of his Barca wages, he pulls in about $21 million in endorsements from sponsors including Adidas, PepsiCo and P&G and is 10th on Forbes’ latest list of top-earning athletes.
According to the charges, Messi and his father created a network of shell companies in tax havens that allowed them to reduce the tax bill on the player’s earnings from selling his image rights, the prosecutor’s office spokesman said.
Messi came on for the final half-hour of Argentina’s World Cup 2014 qualifier against Ecuador in Quito on Tuesday, which ended in a 1-1 draw.
The forward and his Argentina team mates are due to play a friendly against Guatemala in Guatemala City on Friday.