"Judge Pablo Ruz has charged FC Barcelona with an infringement against the tax authority relating to the purchase of the Brazilian player," the spokesman said.
Barca denied wrongdoing after local media reported on Wednesday that Spain's public prosecutor had asked Judge Ruz to lay fraud charges against the club.
"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."
Neymar's high-profile move from Santos in the close season is also being investigated for possible misappropriation of funds following a complaint from a Barca member.
Sandro Rosell, who was named in the lawsuit but denies wrongdoing, stepped down as president last month. He said he wanted to protect the club's image and alleged he and his family had been threatened.
Rosell was replaced by his deputy Josep Bartomeu who said Neymar cost Barca €86.2 million (£71.1 million), including payments to the player and his family, and not €57.1 million as they originally said.
Barca initially refused to reveal all the details of the deal, citing a confidentiality agreement with Neymar's family, but Bartomeu announced that Neymar's father had given them permission to go public.
Image: Neymar
Photograph: David Ramos/Getty Images
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