After president Sandro Rosell stepped down last month following an allegation of misappropriation of funds made by a club member, Barca admitted Neymar had cost 86.2 million euros (£71 million), including payments to the player and his family, and not 57.1 million (£47 million) as they originally said.
"Judge Pablo Ruz has charged FC Barcelona with an infringement against the tax authority relating to the purchase of the Brazilian player (Neymar)," a spokesman for the Madrid court hearing the case said on Thursday.
The judge had requested Barca's tax records relating to the Neymar deal and had asked the tax authority to calculate the scale of the alleged fraud.
Barca denied wrongdoing after local media reported on Wednesday that Spain's public prosecutor had asked the judge to lay charges.
"The club's actions have, at all times, regarding that operation (to sign Neymar) and in line with the available information, been fully compliant with existing law," Barca said in a statement.
The Spanish champions added they would be sending legal representatives to court "in the coming days" to defend their rights and interests.
"At the same time (Barca) states its complete availability to collaborate with the justice authorities in this process, as it has been doing from the first moment, or in any other that might require its intervention."
Barca's institutional problems do not appear to be affecting their results on the pitch and they secured a 2-0 win away to English Premier League side Manchester City in Tuesday's Champions League last 16, first leg.
They are also joint top of La Liga with Real Madrid and Atletico Madrid with 14 games left and through to the final of the King's Cup to face Real.
"We are completely out of it," midfielder Sergio Busquets said at a regular post-training news conference on Thursday.
"We hear things but really we have no idea," added the Spain international.
"The club has put forward its side of the story and we support it. Our job is to play matches."
Neymar himself, who turned 22 this month, has defended his father over the transfer deal, arguing he had the right to profit from it and had done nothing wrong.
Neymar recently returned from a month-long injury layoff and came on in the second half of the City game when he set up Dani Alves to score Barca's second goal.
After he quit as president, Rosell was replaced by his deputy Josep Bartomeu, who was closely involved in the protracted transfer negotiations.
The court spokesman said Judge Ruz had also accepted a complaint by a Spanish non-governmental organisation that fights corruption called "Clean Hands".
The complaint accuses Rosell, Bartomeu and another Barca vice president, Javier Faus, as well as Neymar's father, of misappropriation of funds and document fraud.
- Sports & Recreation
- Sandro Rosell
- misappropriation of funds