The club were forced to backtrack having initially said the Brazilian forward arrived at the Nou Camp for 57.1 million euros (46.41 million pounds) after the case was taken to court by a fan seeking to reveal the full figures.
The club then said the deal was nearer to 100 million euros, and the prosecution case against them refers to unpaid tax on this amount.
Judge Pablo Ruz has called for representatives of the club and Rosell to appear in court on June 13.
They will be asked to "quantify the amount withheld by FC Barcelona for the income payable in relation to the professional athlete Neymar Da Silva Santos for Income Tax of Non-Residents (IRNR) and (regular) income tax", according to a court order.
The non-payment allegation refers to 2.4m euros ($3.27m) for 2011, 6.7m euros for 2013, and the possibility of a further 2.6m euros for 2014.
In February, Barcelona paid an extra 13.5m euros ($18.53m) to the Spanish treasury after they were charged with tax fraud, restating that they had not committed any offence but that the payment was due to a "possible difference of interpretation" over how much was owed.
Rosell, who has denied any wrongdoing, stepped down in January, saying he wanted to protect the club's image.
(Reporting by Tim Hanlon, editing by Ed Osmond)
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