The Russian Investigative Committee said on its website opposition leader Navalny and his brother, Oleg Navalny, allegedly set up a shipping company and billed an unnamed trade company $1.8 million but only shipped $1 million worth of goods.
Alexei Navalny denied the accusations, calling them "complete nonsense" on Twitter.
"I see that I alone am not enough, so they're cracking down on my family?" he wrote.
This is the second criminal case against Alexei Navalny, who had been investigated for allegedly misappropriating state-owned timber worth $522,000 while he was an unpaid adviser to Kirov Gov. Nikita Belykh, a former opposition activist, RIA Novosti reported.
As an anti-corruption blogger, Alexei Navalny has made a name for himself exposing high-level fraud, the report said. He has been among the leaders at anti-Kremlin protests in Moscow since last December.