The Investigative Committee, Russia's top investigative agency, said that Vladimir Yevtushenkov, the head of Sistema holding company, was suspected of involvement in a money-laundering scheme involving oil assets in the province of Bashkiria. Sistema owns the Bashneft oil company, which is based in Bashkiria.
Sistema said in a statement that it considers the charges "totally unfounded" and pledged to fight them.
Russian media reports said in June that Russia's largest oil company, state-controlled Rosneft, considered buying Bashneft. In July, a Moscow court froze Bashneft's stock under a money-laundering probe.
Sechin, who has been placed on the US and the EU sanctions lists over the Ukrainian crisis, was seen as the mastermind behind the 2003 arrest of Russia's then-richest man, Mikhail Khodorkovsky.
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Khodorkovsky's Yukos oil company was broken into pieces and sold in dubious auctions with Rosneft seizing the most lucrative elements.
Khodorkovsky was pardoned by Putin last December after spending a decade in prison.
Some observers drew a parallel between Khodorkovsky's arrest and Yevtushenkov's case.
Even Alexander Shokhin, the head of the Russian Union of Industrialists and Enterpreneurs who usually never crosses the Kremlin's path, said that Yevtushenkov's arrest "undoubtedly looks like Yukos No.2," according to the Interfax news agency.
The 66-year old Yevtushenkov is the founder and majority owner of Sistema. The holding also includes MTS, Russia's largest cellular company, among some 200 other assets.
Forbes magazine has ranked him Russia's 15th richest man with an estimated worth of USD 6.8 billion.