Mogilevich and Nekrasov were charged with evading 50 million rubles ($2 million) in taxes from January 2005 to December 2006, said Alexander Pogonchenkov, Mogilevich's lawyer.
If convicted, they could face up to six years in prison.
Anzhela Kastoyeva, spokeswoman for of the Interior Ministry's Central Federal District branch, confirmed the charges Wednesday, Interfax reported.
Mogilevich was using the name Sergei Shnaider when he and Nekrasov were detained last week in Moscow.
Pogonchenkov explained that his client, who is wanted by the Federal Bureau of Investigation for alleged fraud and racketeering, changed his name after marrying Olga Shnaider, a 33-year-old lawyer linked in the Russian media to Arbat Prestige.
Pogonchenkov said Wednesday that he feared for the health of his client, who is experiencing breathing problems.
The U.S. indictment against Mogilevich dates back to a 2003 case in Philadelphia in which he and two associates were accused of manipulating stock of the Pennsylvania-based company YBM Magnex.
Pogonchenkov has said his client has only Russian citizenship, though unidentified law enforcement sources said last week that he holds several passports.
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