Mascherano, who joined Barca from English club Liverpool in August 2010, is alleged to have sought to conceal earnings from his image rights by using companies set up in the United States and Portugal, the prosecutor's office said.
The 31-year-old is accused of defrauding the authorities of 587,822.01 euros in 2011 and 968,907.76 in 2012, they added.
Mascherano, who made no immediate public comment on the charges, this month paid the money owed plus almost 200,000 euros interest, the office said, and local media reported this could work in his favour if he is found guilty.
Barca did not immediately respond to a request for comment.
Mascherano is the latest high-profile football player to be accused of tax fraud following the likes of his Barcelona and Argentina team mate Lionel Messi, who has been caught up in a similar case involving earnings from image rights.
Messi and his father were accused of defrauding the Spanish state of more than 4 million euros by filing false returns for the years 2006 to 2009. They have denied wrongdoing.
Another Barca player, Brazil forward Neymar, has been named in a lawsuit filed by investment fund DIS that alleges it was the victim of a fraud perpetrated in the signing of the player from Santos in 2013.
Barcelona, former president Sandro Rosell, incumbent Josep Maria Bartomeu, Neymar, his father, Santos and two of the Brazilian club's executives were all named in the suit.
Barca said the club had acted "fully within the law" and rejected the accusations.
In a separate tax evasion case in Brazil, Neymar's parents last week denied any wrongdoing after a judge froze almost $50 million of the player's assets.
Neymar is accused of failing to pay around $15 million in taxes between 2011 and 2013 but his parents said he "cannot declare what is not his" and their son was not a partner in firms a judge said were part-owned by the player.
A Spanish judge must now rule on whether the Mascherano case should go to trial.
(Writing by Iain Rogers, editing by Ken Ferris)
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