The stake in Apatit became part of the Yukos empire following a shady privatization deal more than a decade ago.
The fertilizer producer found itself at the center of a case against jailed oligarch Mikhail Khodorkovsky, the founder and former chief executive of the Yukos giant, in 2003.
Stealing the $283-million asset from the state in 1994 was one of the fraud and embezzlement charges brought against Khodorkovsky and his business partner Platon Lebedev, but it was dropped some way down the 11-month trial as it fell outside a 10-year statute of limitations.
The company is Russia's No. 1 producer of apatite concentrate, a key ingredient in most fertilizers. It develops calcium phosphate mines in the Kola Peninsula, in the Russia's Arctic.
