The Supreme Court thereby upheld an appeal filed by the Prosecutor General's Office. It did not comment on its motives. A district court and the Moscow City Court had earlier upheld the illegitimacy of a new investigation.
Lawyers acting for Khodorkovsky and Platon Lebedev said they would appeal the Supreme Court's ruling at the European Court of Human Rights.
"Everything that has taken place in connection with this case has already been translated into the official languages of the European Court," the former oil tycoon's lawyer, Yury Shmidt, said.
Khodorkovsky and Lebedev, who were convicted of fraud and tax evasion in 2005 and are currently serving eight-year prison sentences, were transferred to a detention center in Chita, east Siberia, last December for a new probe on charges of embezzling government shares, expropriating oil, and laundering $25 billion of illegal oil receipts in 1998-2004.
Both businessmen have denied the accusations, calling them politically motivated.
Khodorkovsky and Lebedev participated in the court session via a video link from Chita.
Once Russia's largest oil producer, Yukos collapsed after tax evasion claims, which led to the company being broken up and sold off to meet debts. The bulk of its assets were acquired by government-controlled oil company Rosneft.