The case has been brought to court by club member Jordi Cases.
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, it was said in court.
"It is not known what has really taken place with the 40 million euros supposedly paid to the player or his representatives," Cases said in a statement read out at the hearing on Wednesday.
The judge Pablo Ruz has given Barcelona five days to provide Neymar's contracts.
He has also asked for the club's financial records from the previous three years to cover the period during which negotiations for the 21-year-old's signing took place.
"It is a charge without basis. I am relaxed," Rosell told reporters on Monday.
Barcelona spokesman Toni Freixa said the club had nothing to hide.
"We have acted with complete transparency and we have nothing to be concerned about," he told a news conference on Monday.
"We have explained the details of the transfer... 40 million euros went to a company. If any judicial body asks for the information then there will be no problem."