He said he would take personal control of the investigation.
In Washington, the White House issued a statement saying the US was "deeply disturbed and saddened by the... brutal slaying".
"Such a heinous crime sends a chilling signal to Russian civil society and the international community and illustrates the tragic deterioration of security and the rule of law in the North Caucasus over the last several months," said the White House.
Ms Estemirova had worked with the Anna Politkovskaya, who was shot dead in 2006, and the activist Stanislav Markelov, who was killed in January this year.
In 2007 she was awarded the inaugural Anna Politkovskaya Prize, and had also received awards from the Swedish and European parliaments.
New York-based human rights group Human Rights Watch (HRW) said Ms Estemirova had been working on "extremely sensitive" cases of human rights abuses in Chechnya.
"There is no shred of doubt that she was targeted due to her professional activity," said Tanya Lokshina, HRW Russian researcher in Moscow.
Campaign group Amnesty International said her murder was a consequence of the "impunity" allowed to persist by the Russian and Chechen authorities, and an attempt to gag civil society in the country.
'Most to fear'
BBC Moscow correspondent Rupert Wingfield-Hayes, who met Ms Estemirova in Chechnya just six weeks ago, says she was engaged in very important and dangerous work.
She was investigating hundreds of cases of alleged kidnapping, torture and extra-judicial killings by Russian government troops or militias in Chechnya.
Our correspondent says it was the government-sponsored militias that had most to fear from her work.
She is the most recent in a long line of human rights activists and lawyers to have been killed or attacked in Russia.
Our correspondent says the history of this type of case over many years is that very rarely are the killers brought to justice.
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