As leaders of FIFA, soccer’s global governing body, gathered for their annual meeting, more than a dozen plain-clothed Swiss law enforcement officials arrived unannounced at the Baur au Lac hotel, an elegant five-star property with views of the Alps and Lake Zurich.

The officers went to the registration desk to get keys, then headed upstairs toward the hotel rooms. One FIFA official was led by the authorities from his room to a side-door exit of the hotel. He was allowed to bring his luggage.

The charges allege widespread corruption in FIFA over the past two decades, involving bids for World Cups as well as marketing and broadcast deals, according to three law enforcement officials with direct knowledge of the case. The charges include wire fraud, racketeering and money laundering, and officials said they targeted members of FIFA’s powerful executive committee, which wields enormous power and does its business largely in secret.

The arrests were a startling blow to FIFA, a multibillion-dollar organization that governs the world’s most popular sport but has been plagued by accusations of bribery for decades.

The inquiry is also a major threat to Sepp Blatter, FIFA’s longtime president who is generally recognized as the most powerful person in sports, though he was not charged. An election, seemingly pre-ordained to give him a fifth term as president, is scheduled for Friday.

Prosecutors planned to unseal an indictment against more than 10 officials, not all of whom are in Zurich, law enforcement officials said. Among them are Jeffrey Webb of the Cayman Islands, a vice president of the executive committee; Eugenio Figueredo of Uruguay, who is also an executive committee vice president and until recently was the president of South America’s soccer association; and Jack Warner of Trinidad and Tobago, a former member of the executive committee who has been accused of numerous ethical violations.

“We’re struck by just how long this went on for and how it touched nearly every part of what FIFA did,” said a law enforcement official. “It just seemed to permeate every element of the federation and was just their way of doing business. It seems like this corruption was institutionalized.”

The Justice Department, the F.B.I. and FIFA did not have any immediate comment.

The case is the most significant yet for United States Attorney General Loretta E. Lynch, who took office last month. She previously served as the United States attorney in Brooklyn, where she supervised the FIFA investigation. Ms. Lynch and F.B.I. Director James Comey were expected to hold a news conference on Wednesday morning in New York.

With more than $1.5 billion in reserves, FIFA is as much a global financial conglomerate as a sports organization. With countries around the world competing aggressively to win the bid to host the World Cup, Mr. Blatter has commanded the fealty of anyone who wanted a piece of that revenue stream. He and FIFA have weathered corruption controversies in the past, but none involved charges of federal crimes in United States court.

United States law gives the Justice Department wide authority to bring cases against foreign nationals living abroad, an authority that prosecutors have used repeatedly in international terrorism cases. Those cases can hinge on the slightest connection to the United States, like the use of an American bank or Internet service provider.

Switzerland’s treaty with the United States is unusual in that it gives Swiss authorities the power to refuse extradition for tax crimes, but on matters of general criminal law, the Swiss have agreed to turn people over for prosecution in American courts.

The case further mars the reputation of FIFA’s leader, Mr. Blatter, who has for years acted as a de facto head of state. Politicians, star players, national soccer officials and global corporations that want their brands attached to the sport have long genuflected before him.

Critics of FIFA point to the lack of transparency regarding executive salaries and resource allocations for an organization that, by its own admission, had revenue of $5.7 billion from 2011 to 2014. Policy decisions are also often taken without debate or explanation, and a small group of officials — known as the executive committee — operates with outsize power. FIFA has for years operated with little oversight and even less transparency. Alexandra Wrage, a governance consultant who once unsuccessfully attempted to help overhaul FIFA’s methods, famously labeled the organization “byzantine and impenetrable.”

Law enforcement officials said much of the inquiry involves Concacaf, one of the six regional confederations that compose FIFA. Concacaf — which stands for Confederation of North, Central America and Caribbean Association Football — includes major countries like the United States and Mexico, and also tiny ones like Barbados and Montserrat.

Concacaf was led from 1990 to 2011 by Mr. Warner, the longtime head of Trinidad & Tobago’s federation. A key powerbroker in FIFA’s governing executive committee, Mr. Warner had been dogged by accusations of corruption. He was accused of illegally profiting from the resale of tickets to the 2006 World Cup, and of withholding the bonuses of the Trinidad players who participated in that tournament.

Mr. Warner resigned his positions in FIFA, Concacaf and his national association in 2011 amid mounting evidence that he had been part of an attempt to buy the votes of Caribbean federation officials in the 2010 FIFA presidential election. A 2013 Concacaf report also found that he had received tens of millions of dollars in misappropriated funds.

But according to the rules of FIFA at the time, Mr. Warner’s resignation led to the immediate closure of all ethics committee cases against him. “The presumption of innocence is maintained,” FIFA said in a short statement announcing his departure.

No recent incident better encapsulated FIFA’s unusual power dynamic than the bidding for the 2018 and 2022 World Cup tournaments, which many observers found to be flawed from the start: the decision to award two tournaments at once, critics said, would invite vote-trading and other inducements.

Since only the 24 members of the executive committee would decide on the hosts, persuading even a few of them might be enough to swing the vote. Even before the vote took place, two committee members — Amos Adamu of Nigeria and Reynald Temarii of Tahiti — were suspended after an investigation by The Sunday Times caught both men on tape asking for payments in exchange for their support. It was later revealed by England’s bid chief that four ExCo members had solicited bribes from him for their votes; one asked for $2.5 million, while another, Nicolas Leoz of Paraguay, requested a knighthood.

As new accounts of bribery continued to emerge — a whistleblower who worked for the Qatar bid team claimed that several African officials were paid $1.5 million each to support Qatar — FIFA in 2012 started an investigation of the bid process. It was led by a former United States attorney, Michael J. Garcia, who spent nearly two years compiling a report. That report, however, has never been made public; instead, the top judge on the ethics committee, the German Joachim Eckert, released a summary of the report. In it, he declared that while violations of the code of ethics had occurred, they had not affected the integrity of the vote.

Within hours, Garcia had criticised Eckert’s summary as incorrect and incomplete, charging that it contained “numerous materially incomplete and erroneous representations of the facts.” Nonetheless, FIFA moved quickly to embrace the report’s absolution of the bid process. Qatar World Cup officials said the review had upheld “the integrity and quality of our bid,” And Russia’s sports minister, Vitaly Mutko, told reporters, “I hope we will not have talk about this again.”