Rosneft is suing Sistema for 170.6 billion roubles ($2.9 billion) in damages over the purchase of oil producer Bashneft. Sistema proposed an out-of-court settlement last week.
Rosneft spokesman Mikhail Leontyev said the arrest of the shares, which halts their use but does not seize them, was a "security measure" and the shares arrested equaled the value of Rosneft claims against Sistema.
Sistema is one of the largest private holdings in Russia and is controlled by businessman Vladimir Yevtushenkov. MTS, with the market value of $8 billion according to Thomson Reuters data, is Sistema's largest asset. Sistema interests also include agriculture, real estate and other assets.
On Monday, Sistema said it had received notice of an enforcement action from the Moscow Directorate of the Federal Bailiffs Service and a copy of a court order from the Republic of Bashkortostan Arbitration Court.
According to the court order, an arrest was imposed on a 31.76 percent stake in MTS, 100 percent of its Medsi chain of medical clinics, and 90.47 percent of Bashkirian Power Grid company owned by Sistema and its unit Sistema-Invest.