Offices of oil giant Yukos in Russia and the Netherlands have been raided as part of an inquiry into allegations that up to $7bn (£4bn) was laundered.
Yukos described the action as "inappropriate" and "unfounded".
Prosecutors said four offices in the Moscow region, as well as a subsidiary in Amsterdam, were involved.
Investigators said they were looking into claims that money was stolen and taken abroad from 2000 to 2003.
Yukos said it was disappointed by the action which it described as "inappropriate" and "unfounded".
Television reports in Russia said that the number of investigators involved was so high that they needed buses to transport them around Moscow.
Mr Khodorkovsky was arrested in October, 2003
Officials also raided the offices of Anton Drel, defence lawyer of former Yukos boss Mikhael Khodorkovsky.
Mr Khodorkovsky - once Russia's richest man - is currently in jail after being found guilty of fraud and tax evasion.
Yukos said in a statement: "It is disappointing to us that despite our efforts to engage with the Russian Federation to find an appropriate solution to this ongoing situation, we are once again the focus of an inappropriate, co-ordinated unfounded series of attacks."
A Yukos spokeswoman in London added that officials had raided the firm's subsidiary in Amsterdam, which owns its foreign assets.
The company said the Dutch Ministry of Justice had not given any explanation for the raid.