Lt. Col. Dmitry Pavlyuchenkov, who was detained Tuesday, also is suspected of supplying the killer a weapon in the fatal shooting of Politkovskaya, RIA Novosti reported.
"The investigation has information about the alleged organizer of the crime although it is too early to make this information public," said a spokesman for the Investigative Committee, which is separate from the police force.
Politkovskaya won widespread acclaim for her reporting on human rights abuses in Chechnya for the newspaper Novaya Gazeta.
Dmitry Muratov, editor in chief of the Novaya Gazeta, had praise and criticism for investigators.
"Pavlyuchenkov's arrest is a success for the Investigative Committee, the Prosecutor General's office and we made our small contribution too," Muratov said.
But he said investigators had not had enough time to fully investigate to be sure they had determined who organized the murder.
"To me, it seems that this work was improperly done and politically motivated," Muratov said.
Politkovskaya was fatally shot in her apartment building in Moscow.
Authorities detained the main suspect in the murder, Rustam Makhmudov, in Chechnya in May.
Three others had been detained in the murder and acquitted for lack of evidence in 2009. But Russia's Supreme Court later overturned the verdict and ordered a retrial