The prosecutor had written to the judge overseeing a probe into the deal, accusing FC Barcelona of drawing up "pretend contracts" and engaging in "financial engineering" to defraud the tax man of 9.1 million euros ($12.5 million), according to the reports which did not identify the source of their information.
A spokeswoman for the prosecutor's office said she was unable to comment on the veracity of the reports.
"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," FC Barcelona said in a statement on Wednesday.
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 (FC Barcelona) 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 already being investigated for possible misappropriation of funds following a complaint from a FC Barcelona 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 euros, including payments to the player and his family, and not 57.1 million as they originally said.
FC Barcelona initially refused to reveal all the details of the deal, citing a confidentiality agreement with Neymar's family, but Bartomeu announced Neymar's father had given them permission to go public.