Putin said last week the murder of the reporter, a critic of the Kremlin, was a "disgusting crime". He added the killing did more harm to Russia than her reporting ever had.
The Presidential Council on Promoting Civil Society and Human Rights confirmed receiving a letter of resignation from Orlov, who heads the independent human rights group Memorial.
Supporters of the slain journalist were angered by what they saw as official corruption and abuses, especially in the Kremlin's campaign against insurgents in Chechnya.
Politkovskaya was shot dead on October 7 in a contract-style killing that investigators said was probably linked to her reporting on Chechnya.
Remembering Anna Politkovskaya
Anna Politkovskaya at RFE/RL in July 2006 (RFE/RL)
A BRAVE VOICE SILENCED. Prominent Russian journalist Anna Politkovskaya was killed on October 7 in her Moscow apartment building. An outspoken critic of the Kremlin, she was best-known for her reporting on the conflict in Chechnya. Former Soviet President Gorbachev called her slaying "a true political homicide, a vendetta."