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Sistema controlled Bashneft until 2014 when the government seized its stake, saying Bashneft's privatisation had been illegal. Rosneft bought a controlling stake in Bashneft from the government in 2016 and in May filed the lawsuit seeking compensation from Sistema, saying assets were removed from Bashneft.
Sistema has rejected these claims as groundless.
The court battle has hit Sistema shares and rekindled broader fears about investor rights in Russia. Rosneft is headed by Igor Sechin, a close ally of President Vladimir Putin and one of the country's most influential businessmen.
Sistema shares have almost halved in price since early May, when Rosneft lodged its claim. After Wednesday's verdict, the shares fell by around 3 per cent in Moscow, while Sistema global depositary receipts in London were up 2.5 per cent.
Sistema spokesman Sergei Kopytov said the company would appeal the decision by an arbitration court in the city of Ufa. "On the whole, the process has been one-sided without any impartiality at all, which had predetermined today's ruling," he said.
The amount the court ordered Sistema to pay was less than Rosneft's initial claim of almost 171 billion roubles. A Rosneft spokesman said the company was satisfied with the ruling but would decide on whether to pursue further damages once the court publishes its full verdict. In June the court froze more than $3 billion of Sistema'sassets, including part of its 50 per cent stake in telecoms company MTS as an interim measure while considering Rosneft's lawsuit.