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The 25-year-old Argentina international and four-time World Player of the year said he had just learned through the media of the allegations filed by the Spanish tax authorities.
"We are surprised about this news because we have never committed any infringement," he said in an English-language statement released on his Facebook account.
"We have always fulfilled all our tax obligations, following the advice of our tax consultants who will take care of clarifying this situation," he said.
Spanish financial crime prosecutors filed the complaint accusing Messi earlier in the day, a judicial source said.
The filing reportedly included the player's father, Jorge Horacio Messi.
"It is all a mistake, you have to speak about this to the tax experts and lawyers who need to clear it up," the father told Spanish sports daily AS.
"I don't understand what is going on. I don't manage these matters, I am resident in Argentina," he was quoted as saying.
The striker's father said he had not spoken to his son about the reports. "I don't need to since it is a mistake. Why would I shock him?"
The court in Catalonia, where Messi is resident, could yet refuse to let the complaint proceed, the judicial source told AFP.
But if it were to go ahead, it would represent a huge blow to the prestige of Messi, who has long been seen as a more humble figure than most top-class footballers and particularly his Real Madrid rival Cristiano Ronaldo.
Messi's achievements on the field have made him one of the most marketable sportsmen in the world, however.
Indeed, the Argentine was ranked 10th amongst Forbes' list of sports stars' incomes this month with an annual $21m from endorsements alone.
Barcelona declined to comment.
The player and his father are accused of three crimes of defrauding the state of taxes related to income from the use of his image in tax declarations made in 2007, 2008 and 2009, Spanish media said, citing a written copy of the filing.
The striker and his father allegedly avoided taxes by pretending to cede their image rights to companies based in tax havens such as Belize and Uruguay.
They are also accused of deliberately setting up image rights deals in Britain and Switzerland, which are reportedly less stringent on the use of corporate tax havens.
Messi and his father acted with "total opaqueness" towards the Spanish authorities, the filing said.
The complaint lodged with the court in Gava, near Barcelona, accused them of defrauding the state of €1.06 million in 2007, €1.57 million in 2008, and €1.53 million in 2009.
The father is accused of being the brains behind the scheme, allegedly setting it up in 2005 before his son turned 18 on June 24 of that year, Spanish media said.
The prosecutor alleged that Messi later agreed with his father's tactics so that he would avoid any taxes on income from the use of his image rights during the period.
The income related to his image rights included contracts with Barcelona, Banco Sabadell, Danone, Adidas, Pepsi-Cola, Telefonica and Kuwait Food Company, media said.
Messi's net income from image rights reportedly amounted to €2.56 million in 2007, €3.82 million in 2008 and €3.80 million in 2009.
