Yury Volkov and Anna Tuchkina, the heads of Gonkar Investment and the Audiyentsiya company, were charged with embezzling and laundering 276 million rubles ($11.7 million) in 2004 after Yukos founder Mikhail Khodorkovsky's arrest on fraud and tax evasion charges.
Investigators said the money was used to pay Khodorkovsky's legal bills.
The Kommersant daily said on Tuesday that Volkov and Tuchkina were initially witnesses in the case against their former chief, Igor Goncharov, who was sentenced in 2005 to 13 years in prison for his role in embezzling and laundering Yukos funds.
The Investigation Committee at the Prosecutor General's Office said the suspects had opened bogus charity organizations across the country in 2004, using the organizations to transfer hundreds of millions of rubles of Yukos funds.
"The money was then cashed and sent to Mikhail Trushin, vice president of Yukos Moskva," said Vladimir Markin, in charge of the committee's press service. "Volkov and Tuchkina thereby stole 276 million rubles."
Trushin fled to London in 2004 and has since been on the wanted list in Russia.
Similar charges were also brought against autocross car racer Vladimir Sorochinsky. He was charged with stealing 20 million rubles (about $846,000) from Yukos as part of a complicated scheme involving financial assistance for his auto club.
The suspects have not been taken into custody, but have given a written pledge not to leave their places of residence.
Commenting on the charges, their lawyers said, as quoted by Kommersant, that investigators had decided "to squeeze some more dividends from the long-running and high-profile case."
The probe against the chief and other executives of what was once Russia's largest independent oil producer was widely criticized in the West and seen as part of the Kremlin's drive to regain lucrative energy assets. Khodorkovsky said the charges were 'punishment' for his support of the country's tiny opposition movement.