Barcelona face charges of corruption over payments made to Jose Maria Enriquez Negreira, a former vice-president of the committee, in return for favourable refereeing decisions.
Uefa is also investigating the matter.
Barcelona deny any wrongdoing and no arrests were made during the search in Madrid.
The Spanish Civil Guard searched the Spanish Technical Committee of Referees (CTA) headquarters on Thursday.
The initial criminal investigation was brought by the Barcelona public prosecutor's office in March, with European football's governing body Uefa launching its own investigation shortly after.
It is alleged that Barcelona paid 8.4m euros (£7.4m) to Negreira and his Dasnil 95 company.
The payments were initially investigated as part of a tax probe into the company run by Negreira.
Barcelona made payments to the company totalling a reported 1.4m euros (£1.2m) between 2016 and 2018, and paid Negreira about 7m euros (£6.2m) between 2001 and 2018, the year he left his role with the referees' committee.
Barcelona acknowledged they had paid Dasnil 95, which it described as “an external technical consultant”, to compile video reports on referees “with the aim of complementing the information required by the coaching staff”.
They said paying for reports was “a habitual practice among professional clubs”.
In February 18 of the 19 other La Liga clubs issued a statement expressing “deep concern”.
In July Uefa provisionally cleared Barcelona to play in this season's Champions League while its investigation is ongoing.