The Spanish champion said in a statement it had paid the "complimentary" amount to cover any "eventual interpretations that could come out of the contracts signed relating to the transfer of Neymar. Meanwhile we are convinced of the legality of our initial fulfilment relating to our tax obligations."
Barcelona's actions take the price of Neymar's transfer to more than 100 million euros ($138 million) after the Catalan club initially said it had paid 57.1 million euros ($74 million) for the Brazil forward.
That sum does not include bonus payments made by Barcelona or the 22-year-old's salary, meaning his total cost likely exceeds the record-breaking 100 million euros-plus spent by rival Real Madrid on Gareth Bale last summer.
Spanish tax authorities had charged Barcelona with fraud on Thursday, alleging it swindled the state of 9.1 million euros ($12.5 million) through payments to varying companies and false contracts.
Barcelona said it had "scrupulously" met its financial obligations in signing the player from Brazilian club Santos and it would continue to work with the state authority in the matter.
Neymar's signing forced the resignation of Sandro Rosell as president last month, after one club member's petition to learn more about the intricate details of what has become a club-record signing were kept in the dark.
Rosell has preached financial prudence while signing lucrative sponsorship deals that have put advertising on the front of Barcelona's jersey for the first time in the history of an institution that considers itself "more than a club" and a symbol of Catalan values.
Rosell is being investigated by the same Spanish court that laid the fraud charges against the club.
Of the initial transfer fee, Brazilian club Santos received 17.1 million euros ($23 million) while Neymar's father, who also goes by Neymar, earned 40 million euros ($55 million).
Barcelona said the decision to make the payment came after an emergency board meeting on Sunday.