A member of the fan-owned club, currently the Spanish league leaders, has lodged a complaint against its president Sandro Rosell alleging misappropriation of 40 million euros out of the total fee paid for Neymar.
Contracts shown to the courts by the club support "doubts raised in the complaint over the signing", public prosecutor Jose Perals said in a court filing.
He called on the National Audience, Spain's highest criminal court, to launch a judicial investigation into the complaint.
Barcelona has said it paid a total €57 million to sign Neymar Da Silva Santos Junior from Brazilian club Santos in June, but it declined to give full details, citing a need for confidentiality.
The complaint accuses Rosell of misappropriation of funds because members do not know the "real destination" of €40 million supposedly paid to Neymar family business N&N, according to court documents.
The prosecutor said contracts shown to the court by the club on the judge's orders contained conflicting details about what exactly the €40 million were paid for.
"All this justifies at least an investigation into whether the allegations in the complaint are true," he wrote.
The prosecutor called on the judge to ask soccer's governing body FIFA to get hold of more documentation related to the signing, including contractsvfrom Santos.