Khelaifi, Valcke and the unnamed businessman are collectively suspected of bribery, fraud, criminal mismanagement and forgery of a document, in a criminal proceeding - effectively an investigation rather than charges - ongoing since 20 March this year.
Former FIFA general secretary Jerome Valcke has denied allegations he received "undue advantages" from Paris Saint-Germain president Nasser Al-Khelaifi in connection with awarding media rights for future World Cups.
Last year, The Office of the Attorney General of Switzerland (OAG) said it was investigating Valcke for "various acts of criminal mismanagement".
"I just want to say that it's not true".
"I refute the accusations against me or Nasser". I have never done that.
beIN Sports, formerly Al-Jazeera Sports, is one of the most powerful broadcasters in world football, owning broadcast rights across the Middle East and North Africa including for Champions League and European Championship matches. I have received nothing from Nasser, I can assure you.
As part of the Swiss OAG's criminal probe, the Paris offices of beIN Sports were raided on Thursday, the French financial prosecutor's office confirming that two of its representatives, along with other French officials dealing with anti-corruption and tax avoidance affairs, had carried out the search.
"There was a contract and Mr Valcke paid the rent", Stephane Ceccaldi said.
In a statement, beIN Media Group said: "Following a request by the OAG of Switzerland, the beIN Sports offices in Boulogne-Billancourt were searched this morning".
The investigation into Al-Khelaifi was reportedly opened in March 2017 and is being conducted in partnership with French, Greek, Italian and Spanish authorities.
Meanwhile, another inspection campaigns were launched in Greece, Italy, and Spain in the framework of the Swiss criminal investigation on the crime of bribing Valcke to buy TV rights to World Cup tournaments.
As a result, he was sacked by FIFA and banned from football for a period of 12 years in January 2016, which was reduced to 10 years in June.
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