The company, which owns 20% of Sibneft, said it would use the entire amount of over 12 billion rubles ($417 million) "to continue paying its alleged tax liability to the Russian authorities."
According to the firm's statement, "Yukos still maintains that the tax claims are illegal and is pursuing all its legal options. The remaining tax liability, after applying the latest payment, will be approximately $6.3 billion of the initial $27.5 billion."
Yukos' founder, Mikhail Khodorkovsky, is serving an eight-year sentence for fraud and tax evasion, while the company itself was forced to sell its main production unit Yuganskneftegaz, ultimately to Russian state oil firm Rosneft, to help pay its tax bills.
The company is currently also in the process of selling its 53.7% stake in Lithuania's Mazheikiu Nafta oil complex, where it is the operator. Kazakhstan's KazMunaiGaz is among the companies keen to buy the stake, which is likely to attract bids in excess of $1 billion.