The Moscow City Court refused to grant the Prosecutor General's appeal against a Moscow court ruling.
Khodorkovsky's lawyer Yury Shmidt said his client and Lebedev will soon be transferred to Moscow.
"In line with the law the trial should certainly be held in Moscow and the guys [Khodorkovsky and Lebedev] should be transferred to Moscow soon," Shmidt said.
In mid-December of last year, Khodorkovsky and his business partner Lebedev were transferred to a pre-trial investigation center near the city of Chita at the demand of the Prosecutor General's Office.
On March 26, Moscow's Basmanny Court rejected an appeal by Khodokovsky's and Lebedev's lawyers demanding that their defendants be transferred to a Moscow pre-trial detention center from Siberia on grounds that the hearing into the new case should be held where the alleged crime took place.
Khodorkovsky and Lebedev, both of whom are serving eight-year sentences in Siberia for fraud and tax evasion, were charged with money laundering February 5.
The Prosecutor General's Office is now accusing Khodorkovsky and Lebedev of stealing $32-billion-worth of oil from Samaraneftegaz, Yuganskneftegaz and Tomskneft in 1998-2003, which the two businessmen allegedly documented as "oil-well liquid."
Prosecutors said Khodorkovsky and Lebedev later resold the oil to end customers for triple the price via bogus firms registered both inside and outside Russia. The scheme helped launder a total of 450 billion rubles ($17 billion) and $7.5 billion, prosecutors said.
The Prosecutor General's Office also alleges that Khodorkovsky and Lebedev are guilty of embezzling receipts from Yukos subsidiaries Fargoil and Ratibor, and of laundering the money through the Open Russia Foundation, a charitable organization established by Khodorkovsky in 2001 as a private endowment to assist academic institutions and non-governmental organizations in Russia.
Khodorkovsky, who acquired oil assets through controversial privatization deals in the early-1990s, has insisted his prosecution was orchestrated by the authorities to silence his criticism of President Vladimir Putin and as part of a campaign to bring mineral assets under Kremlin control.