“In corporate prosecutions, there’s been enormous criticism of the Department of Justice for charging entities not individuals, and this is a flip of that,” said Antonia M. Apps, a lawyer with Milbank, Tweed, Hadley & McCloy and former federal prosecutor for the Southern District of New York. “The confederations and FIFA are treated as victims rather than perpetrators. The indictment says these organizations had good goals and good purposes, and they were co-opted.”

Ms. Apps said it could have been possible for prosecutors to take a different approach and charge FIFA, Concacaf and Conmebol, the organization overseeing soccer in South America. Their nonprofit statuses were unlikely to affect a decision not to, she said. And, certainly, the soccer federations have been sued before — including in Florida State Court by two sports marketing companies that were separately charged by the United States for their roles in the corruption.

But the mission of FIFA and its members might have protected them from prosecution, Ms. Apps and other legal experts said. Their purpose — to regulate and promote soccer throughout the world — was not served by the alleged schemes in the way the bottom line of a bank or a carmaker might have benefited from employee crimes such as violating economic sanctions or failing to report a vehicle safety defect to regulators.

“It’s not a bank, it’s the game of soccer, and its purpose isn’t to maximize profit to stakeholders,” said Serina Vash, executive director of the program on corporate compliance and enforcement at New York University’s law school and a former federal prosecutor in New Jersey. “In order to get the international cooperation the U.S. wanted and needed, they had to focus on individual defendants.”

The people implicated in the case are said to have sought personal gain at the expense of world soccer, violating their duties to act in the interest of FIFA and its confederations. “The government basically says that the Chuck Blazers and Jack Warners of the world acted in a way that deprived the entities of their honest services,” Ms. Apps said, referring to two former Concacaf officials who sat on FIFA’s executive committee.

Made up of six regional confederations with 209 national federations among them, FIFA is a far-reaching conglomerate, which, had it been charged, could have made the United States’ case harder to prove, Ms. Vash said. “The indictment is very carefully crafted to assure it will withstand judicial scrutiny,” she said.