FIFA president Sepp Blatter and UEFA president Michel Platini are facing an investigation by FIFA's ethics committee after the Swiss attorney general opened criminal proceedings against Blatter, according to the Press Association Sport.
PA Sport reports that the ethics committee is looking into the circumstances of a two million Swiss franc (£1.35m) payment that Platini received in 2011 for work said to carried out more than nine years previously.
Swiss prosecutors opened criminal proceedings against Blatter on Friday and Platini was interviewed as a witness by officers from the attorney general's office. Both strenuously deny any wrongdoing.
FIFA presidential candidate Prince Ali of Jordan, Platini's rival for the forthcoming presidential election, said the world governing body has been "shaken to its very core" by the recent scandals.
Platini was a personal adviser to Blatter, his former mentor, when he started out in football politics, and is the favourite to succeed Blatter for the 2016 FIFA presidential elections.
Under Swiss law, a payment is classified disloyal if it is against the best interest of the employer -- in this case FIFA. Platini will have to answer why the alleged payment was not made until nine years down the line.
The Swiss federal prosecutor said police searched and seized data from Blatter's office.
The allegations suggest authorities suspect Blatter of criminal mismanagement of FIFA money to shore up his own power base -- political enrichment, if not taking money himself.
According to the Swiss AG statement, Blatter manipulated FIFA contracts, including one in 2005 with then-Caribbean Football Union president Jack Warner, the former FIFA vice president who was indicted in May on corruption charges in the United States and awaits extradition.
"There is as suspicion that, in the implementation of this agreement, Joseph Blatter also violated his fiduciary duties and acted against the interest of FIFA," the Swiss federal office said.
Blatter's U.S.-based lawyer, Richard Cullen, denied his client's wrongdoing and said he was cooperating, but the statement appeared to focus only on the Warner contract, and not the payment to Platini.
"We are confident that when the Swiss authorities have a chance to review the documents and the evidence they will see that the contract was properly prepared and negotiated by the appropriate staff members of FIFA who were routinely responsible for such contracts, and certainly no mismanagement occurred," Cullen wrote.
Platini released a statement saying he had clarified matters about the payment with the authorities.
"Today I was asked by the Swiss authorities to provide information relating to the ongoing investigations surrounding FIFA," he said on Friday. "I have always been open to supporting the relevant bodies and authorities in their investigative work and therefore cooperated fully.
"Regarding the payment that was made to me, I wish to state that this amount relates to work which I carried out under a contract with FIFA and I was pleased to have been able to clarify all matters relating to this with the authorities.
"I also made clear to the Swiss authorities that since I live in Switzerland I am available to speak with them any time to clarify any matters relating to the investigations."
FIFA, which abruptly cancelled a planned news conference on Friday, said it is cooperating with the Swiss AG office.
German Football Association (DFB) president Wolfgang Niersbach said there was no indication of Blatter's legal troubles when the meeting was cancelled.
"It was not mentioned with one syllable during the ExCo meeting [on Friday]," he said. "I left the FIFA building in the belief that Sepp Blatter will comment on the current situation at the scheduled news conference.
"I only learnt later that the Swiss authorities have opened proceedings against him. The news leaves me speechless."
Blatter is the first person to be formally quizzed as a suspect in the Swiss case, which FIFA instigated last November, when it complained about possible money laundering in the 2018 and 2022 World Cup bidding contests won by Russia and Qatar.
His right-hand man, FIFA secretary general Jerome Valcke, was suspended last week after being implicated in a scheme to sell tickets for the 2014 World Cup on the secondary market.
Warner will face an extradition hearing on Dec. 2 after authorities in Trinidad and Tobago stopped attempts to have the case against him tossed out, officials said last week.