Politkovskaya, who gained international recognition for her strong criticism of the Kremlin and claims of state-backed atrocities against civilians in Chechnya, was gunned down in the entryway of her Moscow apartment building in October 2006.
Putin said the investigation was nearing its final stages and the main suspects had been detained and confessed their involvement in the plot to kill the journalist.
"Some of the detainees have been released, it's true. It speaks about the quality of the investigative work, but in general they are on the right track," Putin said at a news conference after a meeting with German Chancellor Angela Merkel.
Russia's Prosecutor General's Office recently said charges in the Politkovskaya case have been filed against 11 people, nine of whom have been arrested, including several Chechens.
The president said in widely-publicized cases like those of Politkovskaya the investigation should avoid making a hasty announcement of the preliminary results before a court ruling established the suspects' guilt.
"It is necessary to bring the case to a legal conclusion," Putin said. "Until a 'guilty' verdict is issued by a court, all suspects are considered innocent."
