The Blaugrana are embroiled in a legal battle over the Brazilian's transfer to Catalunya but have denied reaching a settlement with prosecutors.
The Catalans were charged with tax fraud following the revelation that 40 million euro of the transfer fee had been paid to the Brazilian's parents.
They later made a "complementary tax declaration" of more than 13m euro and reports Monday suggested they had offered the money to put an end to the case.
However, a statement from the club read: "Following some information published in recent hours, Barcelona categorically deny transferring an agreement to admit an offence against the public treasury to the attorney and thus closing the court case into a tax violation in relation to the signing of Neymar."
The official fee for the Neymar transfer was around €57m while the recently revealed costs before wages ran up to 86.2m euro, but the total could rise depending on payments determined by the current court case.
The former Santos man has scored 12 goals for the Blaugrana since moving to Camp Nou last summer.