Neymar was bought from Santos ahead of the current campaign for a sum of €57.1 million, although reports last month suggested the figure was nearer to €95m.
Barcelona member Jordi Cases subsequently called for an investigation into the club's president Sandro Rosell, who subsequently resigned over the affair and has been replaced by former vice-president Josep Maria Bartomeu.
Spanish media outlets reported on Wednesday that the matter has now caught the attention of the national inland revenue.
However, the club have claimed the transfer was completed with all the relevant documentation and confirmed they will defend themselves against the claims.
A statement read: "In light of reports appearing in today's press concerning the transfer process carried out to bring Neymar to the club, FC Barcelona would like to state:
"1) The club's dealings with respect to this operation, and in light of all information available, was at all times in line with the relevant legal legislation
"2) Represented by its lawyers, the club will appear at the Jutjat Central d'Instruccio (national court of Spain) within the next few days in order to defend its interests and rights.
"3) We express our total willingness to collaborate with the Justice authorities in this matter, as we have done since the first moment the issue arose and in any other area in which our presence may be required."
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