Russian news agencies quoted a source close to the investigation as saying that charges had been framed against Lieutenant-Colonel Pavel Ryaguzov of the FSB, the successor to the Cold War era KGB, for abuse of office.
Ryaguzov was first arrested in August in connection with another case.
The FSB agent is suspected to have passed on the journalist's address to another suspect, who in turn gave it to the killer.
A team of lawyers hired by Politkovskaya's relatives lodged a complaint with a Moscow court, accusing the investigators looking into the journalist's murder of preventing access to the materials of the case.
One of the lawyers said that a local district court is due to hold hearings on the complaint on October 25.
Yuri Chaika, the prosecutor-general, had announced in August the arrest of 10 suspects in the Politkovskaya case.
However, no one was charged at the time and some were later released. Chaika said the killing was planned from abroad by anti-Kremlin forces trying to discredit Russia, but he did not offer any proof.
The Novaya Gazeta, the newspaper for which Politkovskaya had worked, expressed concern when the lead investigator in the case was demoted at the beginning of September.
It said "Kremlin hardliners" were interfering in the case.