A recent investigation found that the Spanish club paid €8.4m (£7.4m) to Jose Maria Enriquez Negreira and his company between 2001 and 2018.
The club, former officials and Negreira were indicted for "corruption", "breach of trust" and "false business records".
Barca described the company as "an external technical consultant" to compile video reports related to professional referees "with the aim of complementing the information required by the coaching staff".
However, 18 of the other 19 La Liga clubs expressed "deep concern" about the revelations, escalating the situation.
La Liga's chief executive Javier Tebas told current Barca president Joan Laporta to resign if he could not explain the payments, as Laporta revealed an internal investigation would be set up.
The public prosecutor's office said: "FC Barcelona obtained and maintained a strictly confidential verbal agreement with Jose Maria Enriquez Negreira so that, in his capacity as vice-president of the technical arbitral committee (CTA) and in exchange for money, the latter carries out actions tending to benefit FC Barcelona in decisions by the referees."
Laporta staunchly denies any wrongdoing, insisting the club has "never bought referees", and dismissed Tebas's comments saying he should resign.