Last month it emerged that Barca have paid Negreira and a company he owns a reported total of 8.4m euros (£7.4m) between 2001 and 2018.
BBC reports a Barcelona court heard on Friday that Barca, former club officials and Negreira had been indicted for "corruption", "breach of trust" and "false business records".
These lawsuits, brought by the Barcelona public prosecutor's office, target the club, as well as former presidents Josep Maria Bartomeu and Sandro Rosell.
La Liga chief executive Javier Tebas said last month that current president Joan Laporta should resign if he was unable to explain the payments.
Laporta responded by saying he will not give Tebas "what he'd like by stepping down" and the charges come three days after Laporta insisted his club had "never bought referees".
"Let it be clear Barca have never bought referees and Barca have never had the intention of buying referees, absolutely never," he said on Tuesday.
How did we get here?
The payments, revealed last month by radio station Ser Catalunya, came to light following an investigation by tax authorities into Negreira's company Dasnil 95.
Barcelona made payments to the company totalling a reported 1.4m euros (£1.2m) between 2016 and 2018, and paid Negreira, 77, about 7m euros (£6.2m) between 2001 and 2018, the year he left his role with the referees' committee.
Barca acknowledged the club had paid Dasnil 95, which it described 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".
It added that contracting the reports was "a habitual practice among professional clubs".
The affair escalated when 18 of the 20 La Liga clubs issued a statement to express "deep concern" over the situation, and Laporta said the club would launch an internal investigation into the payments.
Barcelona coach Xavi, who won eight La Liga titles with them as a player between 1998 and 2015, said he had no knowledge of the payments and never had the feeling his team had any advantage.
"I always wanted to win, but fairly. If I thought we were cheating I'd have gone home," he said after Barca's 2-2 draw with Manchester United in the Europa League last month.
Photo PHOTOSPORT Caption Barcelona FC