Murad Musayev also said the judges had reversed a decision to hold the trial of the suspects in the 2006 murder in a closed court, and that it would be open to reporters.
"The case materials indicate a motive and an individual behind the killing-- anyway a personal motive, which was the critical, revealing reporting by Politkovskaya on certain political figures," he said.
"During the investigation, the prosecutor general said this individual was someone great and terrible based abroad, but the case files indicate that it was someone not so great or terrible - a political figure in Russia," Musayev said, adding his name is not mentioned in the documents.
Top investigators in Russia earlier claimed that fugitive tycoon Boris Berezovsky, who lives in London, was behind the murder.
The head of Russia's Investigation Committee, Alexander Bastrykin, said on Monday that investigators had not identified the person behind the killing, and were continuing to look into several versions.
Three men, Chechen residents, have been charged with involvement in the murder of Politkovskaya, who gained international recognition for reports of military atrocities against civilians in Chechnya and her criticism of the Kremlin.
The journalist was gunned down in an elevator in her Moscow apartment building in October 2006. Police said it was a contract killing. The man suspected of pulling the trigger remains at large. A separate case has been launched against him.
Musayev said the court had reinstated an open trial on the high-profile case to avoid further media pressure.
The trial in the Moscow District Military Court was switched to closed court hearings after the jury reportedly refused to appear in the courtroom last Wednesday in the presence of journalists. However, jury member Yevgeny Kolesov said on Ekho Moskvy radio station the next day the jury had not requested a closed trial.
"The presiding judge took the decision to hold the trial in an open court," Musayev told reporters on Tuesday.
Kolesov left the jury on Tuesday after criticism from the court, which said jurors have no right to discuss an ongoing trial with third parties.
Top prosecutors on Tuesday demanded the replacement of presiding judge Yevgeny Zubov, accusing him of bias, a participant in the trial told RIA Novosti.
"The Prosecutor General's Office has filed for the removal of the judge due to his bias," the source said. He also said the Moscow District Military Court is expected to issue a ruling on the request on Wednesday.
Musayev said the lawyers acting for the suspects and the journalist's family considered changing the judge to be unnecessary.
