Switzerland has opened criminal proceedings against FIFA President Sepp Blatter.
The Swiss prosecutor’s office said Sepp Blatter was suspected of abusing or misappropriating a television rights deal and of “unfair payment” to European football boss Michel Platini.
Sepp Blatter, 79, was questioned and his office searched, he added.
The world’s governing body said it was cooperating with the investigation.
Sepp Blatter has ruled FIFA since 1998 and has always denied any wrongdoing.
Prosecutors say the investigation covers a television rights deal Sepp Blatter signed with former Caribbean football boss Jack Warner in 2005.
“Swiss criminal proceedings against FIFA President Josef Blatter have been opened … on suspicion of criminal misconduct … and – alternatively – embezzlement,” it said.
Sepp Blatter is also suspected of making an “unfair payment” of two million Swiss francs ($ 2 million) in 2011 to Michel Platini, head of UEFA’s European football body, the statement said.
It states that the payment was “at the expense of FIFA, which is alleged to have been made for work carried out between January 1999 and June 2002.”
Sepp Blatter is due to step down in February, and Michel Platini is expected to replace him.
In May, Swiss authorities arrested seven FIFA officials in Zurich at the request of the United States. They are facing extradition.
The United States then uncovered charges against seven other people in their corruption case, nine of whom were high-ranking officials.
Among them was Jack Warner, president of the Caribbean Football Association CONCACAF and one of the most powerful men in world football. He is currently in Trinidad awaiting extradition to the United States on corruption charges.
The Swiss launched their own FIFA investigation hours after the initial arrests.
FIFA owns the World Cup television rights and sells them to regional federations, which then sell them to television operators.
Sepp Blatter’s lawyer, Richard Cullen, said he was confident the investigation would clear Blatter of any wrongdoing over his contract with Jack Warner.
“We are convinced that when the Swiss authorities have a chance to review the documents and evidence, they will see that the contract has been properly drafted and negotiated by the relevant FIFA staff who were routinely responsible for such contracts, and there is certainly no mismanagement , “ he said.
Sepp Blatter won the fifth consecutive FIFA presidential election on May 29, but after allegations of corruption announced his decision to step down on June 2. He is due to end his term at the FIFA extraordinary congress on February 26.
FIFA canceled its press conference on September 25 just minutes before it began.
Sepp Blatter would speak in public for the first time since Secretary-General Jerome Valcke was suspended last week amid allegations of ticket sales for the 2014 World Cup.
Newspaper reports involved Jerome Valke, 54, in a ticket-selling scheme with more than face value.
Jerome Valcke, who described the allegations as “fabricated”, has been released pending an investigation.
Earlier, FIFA also announced that it had moved its next meeting of the executive committee from Tokyo to Zurich.
Correspondents say that although no charges have been filed against Sepp Blatter, he may be more vulnerable to a request for extradition outside Switzerland.