Bartomeu will be expected in court later this year to defend himself against the allegation, along with former president Sandro Rosell, who resigned in January over the signing.
The current chief, previously vice-president to Rosell, and the club are accused of tax fraud to the tune of €2.8 million. Bartomeu has been named in the latest document by the public prosecutor's office and judge Pablo Ruiz has been encouraged to press charges against both he and Rosell.
Barca bought Neymar from Santos in the summer of 2013, but the terms of the deal have caused much controversy.
The Catalan club insisted they had paid €57.1m for the Brazil attacker, but a complaint was lodged against Rosell by Barcelona fan and socio Jordi Cases, alleging misappropriation of funds and a lack of transparency over the €40m allegedly paid to the company owned by Neymar and his father.
Following Rosell's resignation, Bartomeu revealed the official figures at a press conference as Barca confirmed they had indeed paid €40m to the players' parents.
Barca announced the total operation had cost the club a total of €86.2m: €57.1m euros for the transfer itself (of which €40m went to the player's parents), €10m as a signing-on fee, €2.7m in commission, €4m in marketing, €2.5m for Neymar's foundation and €9.9m in scouting and collaborative deals with Santos.
However, alleged unpaid taxes of around €12.1m mean the sum stands at closer to €100m now, even though Barca maintain the total transfer fee remains the €57.1m they originally quoted in 2013.
