The court in the Siberian city of Chita, where the former oil tycoon is serving his eight-year sentence on fraud and tax evasion charges, issued the ruling after hearing the defense team and the prosecution's arguments at sessions on Tuesday and Thursday.
Khodorkovsky accused investigators at the Prosecutor General's Office of concealing evidence substantiating his innocence and continuing the probe after it was officially closed.
In his 30-point complaint, Khodorkovsky also said prosecutors had failed to notify him of a new probe launched on December 2004, which he only learned about two years later when brought for interrogation.
Lawyer Boris Gruzd said at the hearings in Chita that his client had "in effect been denied the right to legal defense."
Prosecutors insisted their actions were legitimate.
The latest charges against Khodorkovsky and his former business partner Platon Lebedev, both convicted in 2005, include stealing government shares, illegal oil trading, and laundering $25 billion earned from oil sales in 1998-2004.
Both have maintained their innocence of all the charges. Khodorkovsky said his imprisonment was a direct result of his support for Russia's tiny pro-Western opposition.
Yukos, once Russia's largest independent oil producer, collapsed after claims of tax evasion in 2004 which led to the company being broken up and sold off to meet creditor claims. The bulk of its assets were bought through liquidation auctions by government-controlled oil company Rosneft. The company was officially dissolved in 2007.
