The ministry said Thursday a European court ruling that awarded billions of dollars in compensation to former shareholders of the company was unjust.
"The Russian Ministry of Justice does not regard this court ruling as an example of a fair and impartial approach to assessing all legal and factual circumstances of a case," the ministry said.
The European Court of Human Rights ruled Thursday the Russian government had to pay shareholders of Yukos around $2.6 billion in damages.
The court said "that Russia had to produce, in co-operation with the Council of Europe's Committee of Ministers, within six months from the date on which the judgment became final, a comprehensive plan for distribution of the award of just satisfaction."
The Permanent Court of Arbitration in The Hague ruled Monday the Russian government is liable for around $50 billion in damages in the case against Yukos, disbanded in 2006.
Former Yukos head Mikhail Khodorkovsky was arrested in 2003 and convicted of tax evasion and theft in 2005. The company was then sold off, with most of the shares going toward Russian state-owned oil company Rosneft, controlled by Igor Sechin, a close ally of President Vladimir Putin.
Rosneft itself has been the target of sanctions against Russia's energy sector issued in response to Moscow's stance on crises in Ukraine.