Investigators are examining allegations of bribery surrounding Khelaifi, head of the Doha-based beIN media group, and ex-FIFA secretary general.
Investigators are examining allegations of bribery surrounding Khelaifi, head of the Doha-based beIN media group, and ex-FIFA secretary general, Jerome Valcke, over the sale of World Cup media rights for football's flagship tournament.
"It is suspected that Jerome Valcke accepted undue advantages from a businessman in the sports rights sector in connection with the award of media rights for certain countries at the FIFA World Cups in 2018, 2022, 2026 and 2030 and from Nasser al-Khelaifi in connection with the award of media rights for certain countries at the FIFA World Cups in 2026 and 2030," read a statement from the Swiss attorney general's office.
The Qatar broadcaster strongly denied the claims.
"beIN Media Group refutes all accusations made by the OAG (Switzerland's attorney general's office)," it said in a statement.
Although the investigation is bad news for the high-profile PSG president Khelaifi, thought currently to be in Qatar, it is highly unlikely the fallout will be contained to him and Valcke.
Scrutiny on FIFA and Qatar will intensify as a result, say experts.
"In isolation, it would be easy to explain today's developments as being yet another example of an allegedly dubious practice in a sport characterised by an endless flow of misdemeanours," said Simon Chadwick, professor of sports enterprise at Britain's Salford University.
"However, this is not an isolated incident, and forms part of an ongoing narrative that has built-up around both FIFA and Qatar."
World football is still dealing with the fallout from the events of 2015 when FIFA officials were arrested en masse at the governing body's annual conference.
And Qatar also remains at the centre of the storm engulfing the sport.
The news from Geneva caps a tumultuous few days, weeks and months for Qatar.
Long used to denying graft allegations over its successful bid for the 2022 tournament -- which Qatar has done numerous times -- the Gulf state has been presented with a far different set of challenges since June 5, since the regional diplomatic crisis began.
The diplomatic isolation of Doha following the blockade announced by neighbouring countries such as Saudi Arabia and the UAE has impacted in almost unimaginable ways.
And Thursday's news also places its policy of diplomatic soft power centre-stage.
Qatar has been enormously ambitious and successful in using soft power through sport and the media -- beIN also owns Hollywood's Miramax, for example -- to promote itself on the world stage.
That strategy is increasingly under attack.
Earlier this week, Doha's government communications office took the unprecedented step of stating the 2022 World Cup "was not up for negotiation" after some claims it could be taken from Qatar because of the political crisis.
beIN has also found itself targeted across the Gulf during the crisis where it is a major sports broadcaster in the region, with programmes blocked.
"This development is set against a backdrop of an intense, and an increasingly fractious feud," Chadwick told AFP.
"Hence, the timing and nature of allegations being made against Al-Khelaifi is suspicious.
"One suspects it could be part of an ongoing information war being waged by Gulf rivals."
Probably the greatest example of soft power was the stunning transfer of Brazilian superstar Neymar to PSG, successfully overseen by Khelaifi, earlier this year.
Now though, Qatar may have overreached with that policy.
Khelaifi's connections are undeniable -- he is a tennis-playing friend of the country's Emir Sheikh Tamim bin Hamad al-Thani.
The fact that he has been named is notable.
But high-profile comes at a potential high cost.
"The image and reputation of both Qatar and the region is suffering," Chadwick told AFP.
"The feud is reinforcing preconceptions and stereotypes that many people across the world hold about Gulf nations.
"As such, it seems imperative that all concerned find a quick, consensual solution to what is damaging the region's football and its standing in the world."