The State Attorney is seeking to bring the Barcelona star to trial for evading payment on image rights, but a statement released on Thursday slammed the court's ruling.
Lionel Messi has fiercely criticised the decision by Spanish authorities to press charges against him for tax fraud, a ruling that went against previous recommendations by prosecutors.
Officials investigating the case against Messi and his father Jorge had stated that the player should be excused from accusations, on the grounds that he was unaware of the illegal maneuvers used in the payment of image rights.