Prosecutors accuse FC Barcelona, who currently have a narrow lead at the top of the Spanish league, of irregularities in the 86-million-euro (USD 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 FC 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 FC Barcelona owe the taxman nine million euros (USD 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".
FC 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.