The regional court said on Wednesday it would investigate Barcelona and two of the LaLiga club's former presidents, Sandro Rosell (59) and Josep Maria Bartomeu (60), over the crimes of corruption in sports, unfair administration and falsehood in documents.
After prosecutors filed the complaint on Friday over alleged payments of more than 7.3 million euros from 2001 to 2018 to firms owned by Jose Maria Enriquez Negreira, State Attorney General Alvaro Garcia Ortiz ordered on Tuesday that the case be transferred to anti-corruption prosecutor's office due to the high-profile nature of the allegations that could constitute significant corruption offences.
The Spanish government and Real Madrid said they would join the complaint as soon as the judge took it on.
Negreira was vice-president of the refereeing committee of the Spanish Football Association from 1993 to 2018 under then president Victoriano Sanchez Arminio.
Prosecutors allege that under a secret agreement and "in exchange for money", Negreira favoured Barcelona "in the decisions taken by referees in the games played by the club, as well as in the results of the competitions".
Reuters has been unable to reach Negreira for comment.
A senior Barcelona official told Reuters on Friday the club had expected the prosecutors' complaint and described it as "nothing more than an absolutely preliminary investigative hypothesis".
The official said the club would fully cooperate with the investigation and it reiterated that "they have never bought any referee nor have tried to influence any official's decisions".
In a statement last month the football club denied wrongdoing, saying it had paid an external consultant who supplied it with "technical reports related to professional refereeing". It was a common practice among professional football clubs, it said.
"I am looking forward to confronting all the scoundrels who are tarnishing our shield," Barcelona president Joan Laporta (60) told an event held by the club with the captains of the different Barcelona teams on Monday.
The prosecutors' complaint focuses on 2.9 million euros paid from 2014 to 2018 and alleges that Barcelona, with the help of former presidents Sandro Rosell and Josep Maria Bartomeu, reached a "confidential verbal agreement" with Negreira.