Putin was criticised in Russia and abroad for failing to speak about the murder in public until three days after the event.
When he did speak of it on Tuesday during an official visit to Germany, he called it an "appalling" crime "that cannot go unpunished".
But he went on to say: "I think that journalists should know, and experts perfectly understand, that her capacity to influence political life in Russia was extremely insignificant.
"This murder inflicts far more damage on Russia, on the current authorities in Russia and in the Chechen republic which she worked on professionally recently, than her publications did."
Vitaly Yaroshevsky, the assistant editor of the Novaya Gazeta newspaper where Politkovskaya worked, said: "We're in a cold rage.
"He said that Anna didn't have an influence on society a day after all the foreign papers had her face on the front page and many Russian papers did as well. She was the number one story even on television news channels he controls."
Politkovskaya, who investigated human rights abuses in Chechnya and openly criticised Putin, was shot on Saturday in what police called a professional hit.
"it's completely clear that the murder of Anna Politkovskaya didn't happen in a void - it happened in a country where democratic institutions have been dismantled and freedom of speech eliminated"
Garry Kasparov, opposition politician
Elena Bonner, a human rights campaigner, said: "To say that her publications inflicted damage on Russia is to acknowledge that truth inflicts damage on Russia."
Garry Kasparov, the former chess champion turned opposition politician, said he had little faith in Putin's vow to do "everything necessary" to find the killers.
He said: "The announcement is marked by extreme cynicism, because it's completely clear that the murder of Anna Politkovskaya didn't happen in a void - it happened in a country where democratic institutions have been dismantled and freedom of speech eliminated."
The New York-based Committee to Protect Journalists (CPJ) called Putin's statement a "backhanded attack".
CPJ said in a statement: "Given the political realities in Russia no investigation can succeed without the complete and unequivocal support of President Putin ... his backhanded attack on Politkovskaya's influence and credibility belies his commitment to justice."
Yevgeny Ikhlov, from the Russian non-governmental organisation For Human Rights, said that Putin's comments "acknowledged that her publications did serious harm and damage to the current authorities.
"I had naively thought that they did harm to uniformed butchers and thieves, to bureaucrats who are deaf to the people's suffering," he said.
At least 42 journalists have been killed in Russia since 1991 and, according to CPJ figures, Politkovskaya was the 13th journalist to die in a contract-style killing since Putin came to power in 2000.