The World Player of the Year and his father Jorge allegedly filed fraudulent tax returns for the years 2006 to 2009, according to Jose Miguel Company, a spokesman for the prosecutor's office for tax crimes in Catalonia.
"We learned about the action begun by the Spanish prosecutor through the media," Rosario-born Messi, who has been resident in Barcelona since 2000 and gained Spanish citizenship in 2005, 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."
Via a complex web of shell companies in Uruguay, Belize, Switzerland and the United Kingdom, income from the sale of Messi's image rights was effectively hidden from the Spanish authorities, the prosecutor's office said in a statement.
The pair could face up to four years in jail if found guilty, according to Spanish law.
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.
As well as income he received from the three companies mentioned above, Messi also avoided paying tax on earnings from selling his image rights to the Aspire Academy in Qatar and from a trip he made with Barca team mates to Uzbekistan in 2008, the prosecutor's office 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.
