The FIFA officials are accused of taking "bribes and kick backs" from sports marketing bosses in return for awarding media and sponsorship rights.
Swiss authorities have said they expect the suspects to be deported quickly to face charges in the US.
In a separate investigation, the Swiss prosecutor is investigating allegations of "criminal mismanagement and of money laundering in connection with the allocation of the 2018 and 2022 football World Cups".
Documents and electronic data were seized from FIFA's headquarters in Zurich today.
Ten members of FIFA's Executive Committee who took part in voting for the Qatar and Russia World Cups will be questioned.
The Swiss prosecutor said raids were carried out at the same time to prevent any possible destruction or collusion of evide.
It is understood FIFA president Sepp Blatter, who is standing for re-election on Friday, was not detained in Zurich today.
He is now in crisis talks ahead of a planned press conference.
Police said the bribery arrests were made "without opposition" although some were seen being covered by bed sheets as they were led from the hotel.
A statement from the Swiss Federal Office of Justice (FOJ) read: "The six soccer functionaries were arrested today in Zurich by the Zurich Cantonal Police.
"The FOJ's arrest warrants were issued further to a request by the US authorities."
"The US Attorney's Office for the Eastern District of New York is investigating these individuals on suspicion of the acceptance of bribes and kick-backs between the early 1990s and the present day.
"The bribery suspects - representatives of sports media and sports promotion firms - are alleged to have been involved in schemes to make payments to the soccer functionaries - delegates of Fifa and other functionaries of Fifa sub-organisations - totalling more than 100 million US dollars."
"In return, it is believed that they received media, marketing, and sponsorship rights in connection with soccer tournaments in Latin America.
"According to the US request, these crimes were agreed and prepared in the US, and payments were carried out via US banks."
The FIFA officials charged under the probe are Jeffrey Webb, Eugenio Figueredo, Jack Warner, Eduardo Li, Julio Rocha, Costas Takkas, Rafael Esquivel, José Maria Marin and Nicolás Leoz.
Swiss officials said the suspects' deportation could be sanctioned immediately.
It is understood the US investigation goes well beyond FIFA and will involve sports-marketing executives across Latin America.
An investigator told the New York Times: "We’re struck by just how long this went on for and how it touched nearly every part of what FIFA did.
"It just seemed to permeate every element of the federation and was just their way of doing business. It seems like this corruption was institutionalised."
The investigation is being led by US Attorney General Loretta Lynch, he came into office in February.
She is due to hold a press conference in New York later this morning.
FIFA is also due to hold a press conference at 10am British time.
Prince Ali Bin Al Hussein, who is standing against Sepp Blatter in FIFA's elections, said: "Today is a sad day for football.
"Clearly this is a developing story, the details of which are still emerging.
"It would not be appropriate to comment further at this time."