"Yukos was a serious lesson and would have implications for the economic development for some time," Alexei Kudrin, Finance Minister was quoted as saying by Russian media.
"Of course it contributed to the lowering of trust in the Russian economy," he said, adding, "The period for restoring this trust will take some time."
On Tuesday, a Moscow court sentenced ex-Yukos CEO Khodorkovsky and his business partner Platon Lebedev to nine years prison term each on multiple charges including tax evasion, fraud and cheating.
"Cases similar to the Yukos affair should not be replayed in Russia ever again," Kudrin said, urging both authorities and businesses to act responsibly.
The broad spectrum of the Russian political forces have hailed the Moscow court ruling, although the Communists were reserved in their comments.
"The national wealth accumulated by three generations was plundered in the course of privatisation by a handful of people, however, Yukos was made the scapegoat," Communist leader Gennady Zyuganov said.
In bid to create an anti-Putin front, Khodorkovsky had financed the campaign of several political parties, including the Russian Communist Party opposing the Kremlin. A number of Communist MPs in Duma are former Yukos executives.