The Barcelona star, along with father Jorge, has been accused of evading tax charges over a three-year period and is alleged to owe in the region of €4 million (£3.3m)
The Spanish tax authorities are investigating claims that the four-time Ballon d’Or winner and his father, Jorge Horacio, have avoided paying the charges due from sales of the 25-year-old's image rights by operating through companies based outside of the country.
A complaint, signed by prosecutor Raquel Amado, was filed with the courthouse in the Gava district of Barcelona on Wednesday.
Messi moved quickly to deny the claims, and in a statement released via his official Facebook account, he revealed he had only been made aware of the developments through media channels and not official sources.
He said:"We have learned through the media about the claim filed by the Spanish tax authorities.
"We are surprised about this news, because we have not committed any infringement. We have always fulfilled all of our tax obligations, following the advice of our tax consultants, who will take care of clarifying this situation.”
Under Spanish law, Messi could face a maximum penalty of six years in prison if found guilty.