Politkovskaya, who gained international recognition for her criticism of the Kremlin and reports of military atrocities against civilians in the troubled Caucasus republic of Chechnya, was gunned down in an elevator in her Moscow apartment building in October 2006, in what police described as a contract killing.
The Prosecutor General's Office on Tuesday accused the presiding judge of bias and demanded he be replaced after he ruled that the murder trial could go ahead in an open court.
"The court made this ruling, as far as the state prosecution's arguments are incorrect and are not corroborated by the evidence," Valery Chernikov, lawyer for Pavel Ryaguzov, a defendant in the case, said.
The trial, which was due to be held in an open court, was switched to a closed court last Wednesday after the jury refused to appear in the courtroom in the presence of journalists.
However, jury member Yevgeny Kolesov told Ekho Moskvy radio station Thursday that the jury had not requested a closed trial.
Chernikov also said the Moscow District Military Court had planned that the Politkovskaya murder trial would be heard in 45 days.
Three men, a former police officer and two brothers from Chechnya, have been charged with involvement in the murder. Sergei Khadzhikurbanov, and Dzhabrail and Ibragim Makhmudov have been in custody since last August. Investigators have provided no details as to their alleged roles in the crime.
The man suspected of pulling the trigger, Rustam Makhmudov - the eldest of the three Makhmudov brothers - remains at large. A separate case has been launched against him.
A former Federal Security Service (FSB) officer, Colonel Pavel Ryaguzov, has also been charged with abuse of office after allegedly telling the killers where Politkovskaya lived.
