The focus of the authorities’ search was Mr. Blatter’s office, where he hosts soccer officials, business leaders and even royalty in leather lounge chairs beside a glass-topped table. The décor in the office and a waiting room outside includes a few stuffed animals (mascots from various FIFA events); awards and honors in framed glass cases; and, just outside the office, a replica of the World Cup trophy. If the investigators wanted coffee, Mr. Blatter could have offered them sugar sachets emblazoned with the FIFA logo.

It was the second time that Swiss authorities are known to have searched for and seized data at FIFA’s headquarters. The first came on May 27, when 14 top soccer and marketing officials were arrested in Zurich as they gathered for FIFA’s annual congress. The United States Department of Justice issued the warrants for those arrests, many of which were carried out by the Swiss police at a luxury hotel in the early morning hours. Mr. Blatter was not implicated or charged that day, but Swiss and American officials later said that he was a target of their investigators.

Now, four months later, Swiss authorities are directly investigating Mr. Blatter, who has led FIFA since 1998. His tenure has seen significant growth of the game and the organization’s coffers, but also a variety of corruption scandals.

A United States law enforcement official said Friday’s announcement by Swiss authorities was independent of the Justice Department’s investigation, which continues. But Swiss and American investigators continue to coordinate their efforts, and the teams met just last week.

One part of the case announced Friday involves a contract Mr. Blatter is said to have signed that assigned valuable World Cup television rights to the control of an indicted former FIFA official, Jack Warner, for far below market value. Mr. Blatter is accused of violating his fiduciary duty to FIFA in his role as president by signing the contract in 2005, which the Swiss authorities called “unfavorable to FIFA.”

The contract, obtained by the Swiss broadcaster SRF, which posted excerpts on its website, awarded the Caribbean Football Union, which Mr. Warner controlled, the rights to the 2010 and 2014 World Cups for a total of $600,000. Mr. Warner, in turn, licensed those rights for roughly 33 times that amount, or about $20 million.