The Brazil forward signed for the Spanish champions in the close season for 57.1 million euros, of which 17.1 million euros went to his former club Santos.
Barca club member Jordi Cases filed a complaint seeking clarification over what happened to the remaining 40 million euros and on Friday the state prosecutor asked the judge overseeing the case to open proceedings against Rosell, who denies wrongdoing.
The judge has yet to rule on the prosecutor's request.
"Barcelona Football Club wishes to express its most energetic indignation about the report by the state prosecutor on the signing of Neymar Da Silva Santos Junior," Barca said in a statement on their website (www.fcbarcelona.es) on Saturday.
"The operation to sign Neymar Da Silva Santos Junior was complex, an example of business engineering, and we have repeatedly expressed the confidential nature of some of its agreements," they added.
"Our rivals were prepared to conduct the same operation for much more money but (FC Barcelona) won through thanks to the skill and expertise of its negotiating team.
"This contractual complexity, labelled by the prosecutor in his report as 'contractual simulation', never constitutes a crime in itself.
"We believe the prosecutor is making a mistake in believing otherwise. Faced with the seriousness of these facts, and despite a belief in the good faith of the legal authorities, we will act forcefully to defend the honour of (FC Barcelona) and its president.