Fifa president Sepp Blatter has been questioned by Swiss federal police over alleged financial corruption.
The attorney general's office in Switzerland said it has opened criminal proceedings against Mr Blatter over possible criminal mismanagement and misappropriation of Fifa money.
The Swiss federal office said Mr Blatter was interrogated after chairing a meeting of Fifa's executive committee today.
Fifa vice-president Michel Platini was questioned as a witness over a suspected "disloyal payment" of two million Swiss francs he allegedly received from Mr Blatter in February 2011, Swiss authorities said.
Under Swiss law, a payment is classified as disloyal if it is against the best interests of the employer - in this case Fifa.
Officers from the Swiss Office of the Attorney General (OAG) interrogated Blatter at FIFA headquarters following a FIFA executive committee meeting on Friday. His office was searched and data seized.
An OAG statement said: "Swiss criminal proceedings against the president of FIFA, Mr. Joseph Blatter, have been opened on September 24, 2015 on suspicion of criminal mismanagement and - alternatively - misappropriation.
"On the one hand, the OAG suspects that on 12 September 2005 Mr. Joseph Blatter has signed a contract with the Caribbean Football Union (with Jack Warner as the president at this time); this contract was unfavourable for FIFA.
"On the other hand, 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 and/or FIFA Marketing & TV AG.
"Additionally, Mr Joseph Blatter is suspected of a disloyal payment of 2 million CHF [Swiss francs] to Michel Platini, president of UEFA, at the expense of FIFA, which was allegedly made for work performed between January 1999 and June 2002; this payment was executed in February 2011.”
The statement added: "Representatives of the OAG interrogated the defendant Joseph Blatter following a meeting of the FIFA executive committee. At the same time, Michel Platini was heard as a person asked to provide information.
"Furthermore, the OAG conducted on September 25 a house search at FIFA headquarters with the support of the Federal Criminal Police. The office of the FIFA president has been searched and data seized.
"As for all defendants, the presumption of innocence applies for Mr Joseph Blatter."
FIFA said it was co-operating with the investigation.
A statement said: "Since 27 May, 2015, FIFA has been co-operating with the Office of the Swiss Attorney General (OAG) and has complied with all requests for documents, data and other information. We will continue this level of co-operation throughout the investigation.
"Today, at the Home of FIFA, representatives from the Office of the Swiss Attorney General conducted interviews and gathered documents pursuant to its investigation.
"FIFA facilitated these interviews as part of our ongoing co-operation. We will have no further comment on the matter as it is an active investigation."
Mr Platini is the favourite to succeed the outgoing Mr Blatter as Fifa president next February.
Mr 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 2018-2022 World Cup bidding contests won by Russia and Qatar.
The allegations also relate to World Cup broadcasting contracts Mr Blatter agreed to with former Fifa vice-president Jack Warner in 2005.
"There is a 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.