The court has also ordered the two clubs, as well as members of Neymar's family, Santos officials and Barcelona president Josep Maria Bartomeu and his predecessor Sandro Rosell, to be sent to trial over the controversial transfer.
Altamiro Bezerra, an advisor to NN Consultoria remains hopeful that any charges of corruption shall be absolved.
The case stems from a complaint made by Brazilian company DIS, which owned 40 per cent of the rights to Neymar when he was at Santos.
It argues it lost out on its rightful cut from the transfer because the true value of the deal was understated.
Even if Neymar were to be found guilty, he is unlikely to serve a prison term, with sentences of under two years typically suspended by Spanish jurisdiction.
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The transfer figure originally published by Barcelona was €57.1m (£48.4m) with €40m euros (£33.9m) of that given to his family.
DIS believe it was cheated out of a percentage of their share of the deal, due to collusion between Barcelona, Santos and Neymar.
However, it has since emerged that the actual fee paid for the Brazilian was closer to £71.5m - prompting an investigation by the Spanish authorities over allegations of fraud.
"The Judge has set bonds of €3,429,768 (about R50.9m) as pecuniary liability for Rosell, Bartomeu, Rodrigues, Football Club Barcelona and Santos Football Club, which must be paid by all jointly", the court said in a statement.
Barcelona did not immediately respond to an emailed request for comment.