The indictment, and Wednesday's arrests, was connected to a bribery scandal being investigated by U.S., Swiss and other law enforcement agencies that has plunged FIFA into the worst crisis in its 111-year history.
The Justice Department official, who asked not to be named, noted U.S. Attorney General Loretta Lynch was asked at a news conference this week about the timing of the arrests and said, "we basically resolve cases when the evidence comes together, when they're ready for a resolution."
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Blatter also criticised UEFA, whose president, Michel Platini, had called for his resignation, saying it was not setting a good example to other soccer federations.
He told reporters on Saturday that UEFA had opposed a proposal to set up an independent committee to carry out integrity checks on executive committee members before they could take office.
"This was rejected by UEFA so it couldn't go through," he said. "Even now, the big UEFA doesn't have an independent ethics committee, (but) they should be an example for the other confederations... It's not acceptable."
He did, however, call for the two groups to work together, particularly to protect the World Cup.
"They need FIFA and FIFA needs UEFA," Blatter said.
Britain's Prince William, who is president of the English FA, called on FIFA to reform and show "it can represent the interests of fair play" in a speech at the FA Cup final in London on Saturday.
The prince also backed the decision by former Manchester United chief executive and newly elected FIFA vice-president David Gill to quit the position almost immediately in protest at Blatter's re-appointment.
Blatter played down the impact of the scandal on one of the world's most powerful sports bodies, which takes in billions of dollars in revenue from TV marketing rights and sponsorships.
"These crimes which have been committed are related to North and South America and a marketing company has been mentioned, so I do not see how (FIFA) could be directly affected by this."
"We have always tried, in my tenure of office, to eliminate all these elements or individuals."
Blatter has not been implicated in any wrongdoing, but his critics have argued it is time for him to step down.
His supporters welcomed the outcome of a vote that saw him fend off a sole challenger, 39-year-old Prince Ali bin Al Hussein of Jordan.
That support reflects Blatter's success in expanding FIFA's membership away from soccer's heartlands and in exploiting resentment in Africa and Asia over the perceived arrogance of the game's powerhouse nations in Europe and South America.
Despite Blatter's re-election, the scandal surrounding the investigations into corruption looks set to rumble on.
Platini has raised the possibility, albeit slim, of Europe boycotting the World Cup tournament, soccer's showcase played every four years. There has also been talk of UEFA breaking away from FIFA, although that is also seen as unlikely.
Blatter's future could yet depend on the reaction of FIFA's major sponsors and stakeholders such as Coca-Cola and McDonald's, who have been dismayed by the arrests and U.S. prosecutors announcing indictments of officials and companies.
A senior U.S. Internal Revenue Service official said on Friday he thought there would be further indictments, the New York Times reported, although he declined to identify the remaining targets of the investigation.
An IRS spokesman confirmed that Richard Weber, chief of the IRS unit in charge of criminal investigations, made the remarks and said "the case is open and ongoing."
Separately, Swiss prosecutors are investigating the award of the World Cup finals to Russia in 2018 and Qatar in 2022, decisions that have deepened rifts within FIFA.
The choice of Qatar, a small desert state where summer daytime temperatures rarely fall below 40 degrees Celsius, was especially contentious and went against the advice of FIFA's own technical committee.
Russia and Qatar deny wrongdoing in their bids to host the prestigious tournament, and Russian President Vladimir Putin has accused the United States of meddling in an effort to force Blatter out.