The club are alleged to have paid €1.4m [£1.25m] to a company owned by Jose Maria Enriquez Negreir.
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Mr Negreir was vice-president of the Royal Spanish Football Federation (RFEF) Referees Committee from 1994 until 2018.
According to the report from Cadena SER, Barcelona paid Negreir's company, DASNIL 95 SL, over a three-season period between 2016 and 2018, a fee of €1,392,680 [£1,237,509.57].
Barca's payments stopped in June 2018. The date is said to coincide with Negreir's departure from the Referees Committee.
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It is understood an investigation into the said allegations has already taken place by and been conducted by the Prosecutor's Office.
Negreir has since revealed to investigators that he did not favour Barcelona in any such refereeing decisions.
He did, however, state he gave verbal advise to the club following several issues, including how players should behave in front of referees.
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In an official statement published by Barca, the club have responded to the report outlining each point.
"That in the past FC Barcelona hired the services of an external consultant that supplied the club's technical secretaries with reports in video format of youth players from other clubs in Spain," said the club.
"Additionally, the relationship with that supplier extended to technical reports related to professional refereeing in order to complement the information requested by the first and second team coaching staff.
"This a common practice among professional football clubs. These kinds of outsourced services are now the duty of a professional who works for the Football Department.
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"FC Barcelona is sorry that this information has been released precisely when the team has hit its best form of the season.
"FC Barcelona shall be taking legal actions against those who are trying to tarnish the club's image with possible insinuations against its good reputation."
Following on from the infamous 'Barcagate scandal', that saw several board members arrested, this is now the second scandal in recent times to hit the club.