Colleagues believe her murder was linked to her work reporting on abuses by Russian troops in Chechnya.
Sergei Khadzhikurbanov, one of the suspects, is a former police officer. Two others, Dzhabrail and Ibragim Makhmudov, are brothers from Chechnya.
The committee said the charges against the FSB officer, Pavel Ryaguzov, relate to other crimes.
Authorities have previously accused Ryaguzov of giving Politkovskaya's killers her address.
The committee did not cite an alleged motive for Politkovskaya's killing or specify the suspects' roles in her murder.
A separate probe into Rustam Makhmudov, the suspected gunman who remains at large will continue, the investigative committee said on Wednesday.
Rustam is the oldest of the Makhmudov brothers.
Charges against several others, including Shamil Burayev, the former Chechnya district administrator, were dropped, the committee said.
Politkovskaya's colleagues at the Novaya Gazeta newspaper accused authorities of deliberately undermining the investigation by releasing details about the case before it reached trial.
Dmitry Muratov, the editor of Novaya Gazeta, said that leaks from the investigation allowed the accused gunman to escape arrest.
Muratov said it was too early to say the murder had been solved.
Russian officials have alleged that Politkovskaya's killing was ordered by someone living outside Russia with the aim of discrediting the Kremlin.
Their statements that have been interpreted as alluding to Boris Berezovsky, a former Kremlin insider who lives in London and is now a fierce critic of the government.
Berezovsky, wanted in Russia on embezzlement and other charges, all of which he denies as being politically driven, has said he had nothing to do with Politkovskaya's death.
Novaya Gazeta has said the mastermind is likely in Russia.