The court also ordered PwC to pay the state $480,000.
PwC is facing charges of covering up Yukos's tax shelter schemes and drawing up two different audit reports in 2002-2004.
Investigators from the Russian Interior Ministry and the Prosecutor General's Office last week investigated PwC's Moscow office and seized a number of documents on suspicion of evading 243 million rubles ($9.3 million) in taxes in 2002.
The company protested the seizure, saying the documents had nothing to do with 2002 tax claims and that it had already paid all tax arrears.
Russian law enforcement pressed the 2002 profit tax claim against PwC a year ago. The company has lost three appeals in arbitration courts since, and said it is considering an appeal to the Supreme Arbitration Court.
Russian tax authorities are accusing PwC's Moscow branch of under-reporting profit tax on sums it allegedly paid to offshore PricewaterhouseCoopers Resources B.V., which was supposed to provide financial consultations to clients in Russia.
Tax officials said the consultation services were provided by the company's Moscow branch instead.