The dispute centered on Yukos-Mamontovo and an intricate web of dealings involving three other subsidiaries.
In 1998, the shares of four subsidiaries - Yukos-Mamontovo, Yukos-Maiskoye, Yukos-Pravdinsk and Yukos-Priobye - were loaned to Yukos affiliates and in 1999 were transferred to Yukos in compensation after a contract was terminated.
Lawyers representing Yugansk said Yukos-Maiskoye, Yukos-Pravdinsk and Yukos-Priboye had been merged with Yukos-Mamontovo before the 1999 move and was a cover-up for an illegal gift.
Yukos-Mamontovo owns the equipment used by Yugansk, which became part of state-run oil company Rosneft after an auction was held in 2004 to help clear Yukos's massive tax arrears, which means Yugansk now leases it.
Yugansk's lawyers said the company had to pay 153 million rubles ($5.66 million) a month for the equipment's lease.
Lawyers representing Yukos said in a hearing in a lower court on March 27 that the statute of limitations for the Yukos claim had expired, but the court rejected the argument and the appeals court upheld the ruling.
