Mr. Deripaska, an aluminum magnate with ties to President Vladimir V. Putin of Russia, was a client of Paul Manafort, who for several months in 2016 served as Donald J. Trump’s campaign chairman and in 2018 was convicted of financial fraud and other crimes.
Mr. McGonigal’s lawyer, Seth D. DuCharme, said his client intends to plead not guilty when he appears in federal court in Manhattan on Monday.
“Charlie served the United States capably, effectively, for decades,” said Mr. DuCharme. “We have closely reviewed the accusations made by the government and we look forward to receiving discovery so we can get a view on what the evidence is upon which the government intends to rely.”
The indictment also charged a second man, Sergey Shestakov, 69, a former Soviet and Russian diplomat who later became an American citizen and who worked as a Russian interpreter for courts and government offices. Mr. Shestakov’s lawyer, Bennett M. Epstein, declined to comment.
Mr. McGonigal was arrested on Saturday at about 2 p.m. at John F. Kennedy Airport, according a spokesman for the U.S. attorney’s office in Manhattan, and Mr. Shestakov was arrested at about the same time at his home in Morris, Conn.
Mr. McGonigal’s arrest shocked former colleagues who worked closely with him. They said he primarily investigated Russian counterintelligence and espionage during his lengthy career with the F.B.I. Mr. McGonigal also took on extremely sensitive assignments in the intelligence community, leading an F.B.I. team that investigated why C.I.A. informants in China were being arrested and killed.
The charging of a former or current F.B.I. senior executive appears to be extremely rare. In 2018, Andrew G. McCabe, the former acting and deputy director, was referred for prosecution after the Justice Department inspector general accused him of misleading investigators. But the case was eventually dropped. In 1996, a senior F.B.I. official was charged with obstruction in connection with the deadly 1992 standoff in a remote section of Idaho called Ruby Ridge. Nearly two years earlier, the acting F.B.I. director and his deputy, along with another official in charge of counterintelligence, were indicted on conspiracy charges. The charges were the first time an F.B.I. director or former bureau executive had been charged criminally.
Adam Goldman contributed reporting.
Benjamin Weiser and William K. Rashbaum
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