The Russian Investigation Committee alleged on its website Navalny embezzled $3.25 million from the Union of Right Forces in 2007, RIA Novosti reported.
The committee said the Union of Right Forces paid Allekt, a company Navalny headed in 2007, about $3.25 million for an advertising contract, but company transferred the funds to suspected front companies without keeping its side of the agreement.
"No one has provided any documents to the investigation proving that the contract was implemented," the committee said. The charge carries a maximum of 10 years in prison and/or a fine of $32,500.
Leonid Gozman, the former deputy chairman of the Union of Right Forces, said he is unaware of any such theft from their funds.
"If there had really been anything like that, I would have known about it," Gozman told RIA Novosti.
Navalny, who led year-long protests against President Vladimir Putin commented on the allegations by tweeting: "Another criminal case against me. Investigation Committee, what are you doing? Enough."
Pregnant Mila Kunis wins 'Best Villain' at MTV Movie Awards
Biologists detail four new deep-sea 'killer sponges'