According to a Kremlin statement, Mr Putin told US President George W. Bush that "law enforcement bodies will take all necessary measures for an objective investigation into the tragic death."
The brief reaction came 48 hours after Politkovskaya's execution-style slaying and contrasted with a flood of emotional condemnations from world leaders and warnings from human rights organisations over the state of media freedom in Russia.
Politkovskaya, one of Putin's fiercest critics and almost the last Russian journalist still investigating atrocities in Chechnya, will be buried in Moscow later today.
Silent anger
However the Kremlin’s silence has sparked condemnation from two human rights watchdogs, the International Helsinki Federation for Human Rights (IHF) and the Moscow Helsinki Group (MHG).
"The silence of President Putin suggests an attitude of complicity, or of indifference,” said IHF President Ulrich Fischer said in a joint statement.
“No one can accept that, after the country's leading media critic of the government has been murdered, apparently by a professional assassin, he keeps silent."
Germany's foreign ministry called on Russia to protect journalists, saying that "such a crime causes outrage and bitterness and raises deep concerns."
International tributes
British Prime Minister Tony Blair described the slaying of Politkovskaya, 48, as "a terrible crime," while French President Jacques Chirac said he was "profoundly moved and shocked."
The UN High Commissioner for Human Rights, Louise Arbour, also paid tribute to Politkovskaya for her "fearless pursuit of justice in regard to human rights violations in Chechnya and elsewhere."
"Her death is a tremendous loss for the Russian Federation and for all who struggle for human rights around the world," she said.
Every Russian newspaper carried front-page pictures of the bespectacled, prize-winning journalist.
Colleagues at her newspaper, the bi-weekly Novaya Gazeta, published a special issue vowing that "her killers will not sleep soundly."
Even before the killing -- which police say was linked to Politkovskaya's work -- Russia was estimated to be one of the most dangerous places in the world for journalists.
She was the 42nd journalist killed in Russia since the collapse of the Soviet Union in 1991, and the 12th in a contract-style murder since Mr Putin came to power in 2000, according to the New York-based Committee to Protect Journalists.