A spokesman for the Investigation Committee of the Prosecutor General's Office said three men were charged with involvement in the murder and a Federal Security Service (FSB) officer with abuse of office.
Colonel Pavel Ryaguzov was suspected of giving the killers Politkovskaya's address.
The journalist was gunned down in the entranceway of her Moscow apartment building in October 2006.
Vladimir Markin said a separate probe had been launched against the man suspected of carrying out the shooting. Investigators earlier said he remained at large.
Markin said accusations against another suspect in the murder - Shamil Burayev, former head of Chechnya's western Achkhoi-Martan district - were dropped due to lack of evidence.
Markin said the case file would now be made available to Politkovskaya's son, and then to the defendants.
Politkovskaya gained international recognition for her criticism of the Kremlin and reports of military atrocities against civilians in the troubled Caucasus republic of Chechnya.
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