The Times, citing anonymous law enforcement officials, said the U.S. federal charges include racketeering, money laundering and wire fraud and span two decades of misconduct in soccer's world governing body. More than 10 officials were expected to be indicted, the newspaper reported.
The officials are in Switzerland for the FIFA Congress, where incumbent Sepp Blatter faces a challenge from Jordan's Prince Ali Bin Al Hussein in a presidential election on Friday.
FIFA spokesman Walter de Gregorio and Delia Fischer, another spokeswoman for the governing body, were unable to be contacted for verification of the report.
The paper said more than a dozen plain-clothed Swiss law enforcement officials arrived at Zurich's Baur au Lac hotel early on Wednesday, took keys from the registration desk and headed up to the rooms.
One FIFA official was led by the authorities from his room to a side-door exit of the hotel, the Times said, adding that officials from the body's powerful executive committee were being targeted.
"We're struck by just how long this went on for and how it touched nearly every part of what FIFA did," the Times quoted an unnamed law enforcement official as saying.
"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 Times said much of the enquiry was focused on the CONCACAF region, which governs soccer in the North America, Central America and the Caribbean.
The confederation's former boss Jack Warner was regularly dogged by accusations of corruption before he resigned in 2011, putting an end to investigations of the Trinidadian.
Prosecutors expected to announce the case at a news conference at the Brooklyn U.S. attorney’s office, which is leading the investigation on Wednesday, the Wall Street Journal said in a separate report.
U.S. Attorney General Loretta Lynch, Federal Bureau of Investigation Director James Comey and Internal Revenue Service criminal chief Richard Weber were expected to appear in Brooklyn to announce the case, the WSJ said.
The reports offer a fresh blow to the credibility of FIFA, which has suffered repeated accusations of wrongdoing over the bidding process for the 2018 and 2022 World Cups, which were awarded to Qatar and Russia respectively.
FIFA appointed an independent investigator to look into the allegations and though a summary of his report found some wrongdoing on the part of the Qatari and Russian bid committees, FIFA's ethics judge concluded it wasn't enough to question the entire process.
The investigator, former attorney Michael Garcia, subsequently resigned from his role in December after criticising the handling of his report.
(Additional reporting Curtis Skinner in San Francisco and Ian Ransom in Melbourne; Editing by John O'Brien)
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