State Attorney General Alvaro Garcia Ortiz ordered that the case be transferred from the public prosecutor's office due to the high-profile nature of the allegations that could constitute significant corruption offences.
The Spanish government and Real Madrid have joined the complaint filed on Friday by prosecutors against Barcelona and two of the LaLiga club's former presidents over alleged payments of more than 7.3 million euros ($7.83 million) from 2001 to 2018 to firms owned by Jose Maria Enriquez Negreira.
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".
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 "will fully cooperate with the investigation by all means necessary" and "reiterate 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", calling it "a common practice among professional football clubs".
"I am looking forward to confronting all the scoundrels who are tarnishing our shield," Barcelona president Joan Laporta told an event held by the club with the captains of the different Barcelona teams on Monday.
Jose Manuel Franco, president of Spain's Superior Sports Council (CSD), told TV channel Telecinco on Monday it would join the prosecutors' complaint against Barcelona.
"We will join the complaint as soon as the judge takes up the case with the utmost forcefulness. This is not good for Spanish sport. What is bad for soccer is bad for Spanish sport," he said.
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.
It accuses the club, Rosell, Bartomeu, Negreira and two other former Barcelona officials of corruption in sports, unfair administration and falsehood in mercantile documents.