Prosecutors accuse Barcelona, who currently have a narrow lead at the top of the Spanish league, of irregularities in the 86-million-euro ($118 million) deal — charges which the club denies.
Judge Pablo Ruz at Madrid’s National Court indicted the club after seeing “sufficient evidence to investigate a possible crime against the public treasury”, he said in a written ruling.
The judge ordered tax authorities to hand over the club’s tax returns for 2011 to 2013.
He sought to establish whether or not Neymar, who joined Barcelona in May 2013, was counted as a taxpayer in Spain or his native Brazil that year.
The judge also asked tax authorities to provide information about the taxing of deals linked to Neymar’s signing and about how much may have been “defrauded”.
He ordered Neymar’s father, Neymar da Silva Santos, to hand over contracts and documents from various companies linked to the signing.
A court source said separately that the judge had also asked world football’s governing body FIFA to provide information it has about Neymar’s signing.
State prosecutors have alleged that Barcelona owe the taxman nine million euros ($12.5 million) in deals to bring the player to the Spanish champions from Brazilian club Santos.
Prosecutors said on Wednesday that there were “a suspicious number of simulated contracts”.
– Barca defensive –
Barcelona insisted that they have not broken the law at any point during the deal and vowed to clear their name.
“The club’s dealings with respect to this operation… were at all times in line with the relevant legal legislation,” they said in a statement.
The club’s new president Josep Maria Bartomeu vowed to defend the team in an interview with state television TVE.
“We will defend our interests with all the necessary firmness. We are very clear that we have acted well,” Bartomeu said.
“We are going to defend and explain perfectly to all Barca’s members that we are calm, that we have not done anything illegal,” he said.
“We are among those clubs that pay all our debts to the tax collector and in this sense I believe that Barcelona is an exemplary club,” he added.
The club’s former president Sandro Rosell resigned last month over the judicial wrangle sparked by Neymar’s signing, which the club said cost 57.1 million euros.
The case was started by one of Barca’s own members, Jordi Cases.
He accused Rosell of misappropriation for not declaring publicly that 40 million of the 57.1 million figure quoted by Barca was paid to N&N, a company controlled by the player’s parents.
Following Rosell’s resignation, the club revealed that the entire cost of the operation including Neymar’s signing bonus, commissions, marketing deals, a donation to the player’s foundation and other deals totalled 86.2 million euros.
State prosecutors in Brazil have also called on its tax authorities to investigate potential tax fraud.
In an uncharacteristic blast earlier this month, Neymar himself reacted angrily to the controversy.
“I’ve been quiet until now! But I can’t go on listening to all these things about my transfer,” he wrote on the social media network Instagram.
“A lot of people come out and talk a load of rubbish — calling our character into doubt,” he wrote.
“I also understood we have masses of false friends.”
On the field the 22-year-old’s first season in Spain has been disrupted by injuries.
However, he has managed 12 goals in 28 appearances to date and was involved as a substitute as Barca beat Manchester City 2-0 in the first leg of their Champions League last 16 tie on Tuesday.
Barcelona are ahead of their fierce rivals Real Madrid in the Spanish league on goal difference but tied on points with Real and Atletico Madrid.