The 92-count indictment, which includes charges of racketeering, money laundering and wire fraud, expands a corruption case that began in May with charges against 14 officials associated with FIFA and related sports marketing companies.
The announcement came the same day Swiss police arrested two FIFA officials on suspicion of accepting "millions of dollars" in bribes, according to a statement from the Swiss Federal Office of Justice.
Alfredo Hawit, the president of CONCACAF, the governing body for North and Central America as well as the Caribbean, and Juan Angel Napout, president of CONMEBOL, which presides over South America, were the two latest arrests in what is proving a miserable year for the organization in charge of running one of the world's most popular sports.
Its 79-year-old president, Sepp Blatter, and another leading official, Michel Platini -- the Union of European Football Associations president -- are currently suspended for 90 days after the Swiss attorney general opened criminal proceedings.
And in May, 14 executives with ties to FIFA were accused of taking bribes totaling more than $150 million.
Arrests in Zurich requested by U.S.
The Swiss Federal Office of Justice confirmed the identities of Hawit, a Honduran citizen, and Napout, who is from Paraguay, in a statement and revealed they are both opposing their extradition to the U.S.
The arrests in Zurich early Thursday were part of an operation requested by U.S. authorities, as the U.S. Department of Justice prepared to announce a new round of charges against multiple officials and executives tied to alleged corruption at FIFA.
"On the instructions of the (Swiss) Federal Office of Justice, a further two FIFA officials were arrested in Zurich today," the statement read.
"They are being held in custody pending their extradition. According to U.S. arrest requests, they are suspected of accepting bribes of millions of dollars.
"The high-ranking FIFA officials are alleged to have taken the money in return for selling marketing rights in connection with football tournaments in Latin America, as well as World Cup qualifying matches.
"According to the arrest requests, some of the offenses were agreed and prepared in the USA. Payments were also processed via U.S. banks," the statement added, explaining why the U.S. was in a position to ask for the arrests.
The move represents an escalation in the U.S. corruption probe that has already thrown FIFA into disarray.
FIFA released a statement saying it was aware of the arrests of two of its officials.
"FIFA will continue to cooperate fully with the U.S. investigation as permitted by Swiss law, as well as with the investigation being led by the Swiss Office of the Attorney General. FIFA will have no further comment on today's developments."
Accusations of racketeering
In May, U.S. prosecutors unveiled a 47-count indictment
against 14 executives with ties to FIFA and companies with commercial ties to the organization.
They accused FIFA officials of taking bribes totaling more than $150 million and in return providing "lucrative media and marketing rights" to soccer tournaments as kickbacks over the past 24 years.
Those charges included racketeering, wire fraud and money laundering conspiracy.
Swiss police, acting on requests by the U.S., launched predawn raids at a luxury hotel in Zurich to arrest seven of those charged in the May indictments.
Several of those charged have now surrendered to U.S. authorities in New York under agreements to cooperate with the FBI investigation, according to U.S. law enforcement officials.
Separately, Swiss officials have been investigating corruption allegations surrounding the next two football World Cups
. FIFA's flagship tournament is set to be held in Russia in 2018 and Qatar in 2022.
Both Russia and Qatar have publicly denied any wrongdoing with regard to the bidding processes of the two tournaments.