Putin, in televised remarks, accused the U.S. of encouraging and funding the Russians protesting the alleged election fraud in Sunday's elections. By recently describing Russia's election as rigged, Clinton "gave a signal" to his opponents, said Putin, who also warned of a wider Russian crackdown on dissent.
"They heard this signal and with the support of the U.S. State Department began their active work," Putin said. He said the United States is spending "hundreds of millions" of dollars to influence Russian politics with the aim of weakening a rival nuclear power.
Putin's tough words show the deep cracks in U.S.-Russian ties despite President Obama's efforts to "reset" relations with the Kremlin. Ahead of the election, President Dmitry Medvedev threatened to deploy missiles to target the U.S. missile shield in Europe if Washington failed to assuage Moscow's concerns about its plans.
Clinton has repeatedly criticized Sunday's parliamentary vote, saying "Russian voters deserve a full investigation of electoral fraud and manipulation."
Putin's United Russia party barely held onto its majority in parliament, with official results giving it about 50 percent of the vote, down from 64 percent four years ago. But the fraud allegations indicate that support for United Russia was even lower than that, and Russians appear to be growing weary of Putin and his party after nearly 12 years in office.
Putin was president from 2000 until 2008, when he moved into the prime minister's office to abide by constitutional term limits. He intends to reclaim the presidency after an election in March that would give him at least six more years in power.
Putin's return to the Kremlin still seems assured, but he clearly has been shaken by the outburst of public anger and it is not yet clear how much of a challenge it will pose to his power.
Moscow has already put about 50,000 police and 2,000 paramilitary troops on the streets, backed by water cannons.
Putin warned that the government might take an even harder line against those who try to influence Russia's political process on behalf of a foreign government.
"We are the largest nuclear power," Putin said. "And our partners have certain concerns and shake us so that we don't forget who is the master of this planet, so that we remain obedient and feel that they have leverage to influence us within our own country."
He said "especially unacceptable is the infusion of foreign money into the electoral process."
Clinton reached out to Russia on Thursday.
"I think it's important to recognize that we value our relations with Russia," she said at a NATO meeting in Brussels, where she also met with Russian Foreign Minister Sergey Lavrov. "We have invested a great deal of effort on working together ... and we have made progress."
But Clinton defended her criticism of the elections, saying she was expressing concerns the U.S. thought were well-founded.
Russia's only independent election monitoring group, which is supported by grants from the United States and European governments, has come under heavy official pressure in recent weeks. The Golos website documenting violations was hacked and the group was fined the equivalent of $1,000 after prosecutors accused it of violating election law.
Putin's attempt to rally support by blaming the United States for his troubles would find little support among ordinary Russians, said political analyst Dmitry Oreshkin.
"Even in Soviet times, it did not work," Oreshkin said. "Now it won't work for sure."
Also Thursday, Russia's top election official urged prosecutors to study photographs and video clips circulating on social networking sites that purport to show election fraud.
If the images show genuine violations, they will be investigated, Central Election Commission chief Vladimir Churov said. But if evidence is found that the photographs and videos were "provocations" or faked, those who created, commissioned or sponsored them will be held to account, he said.
Opposition groups have called for a mass protest near the Kremlin on Saturday to demand a vote recount. About 30,000 people have now signed up to a Facebook page on the protest.
A map circulating on the Internet shows similar protests planned for Saturday in more than 75 cities around Russia, while a page on LiveJournal lists more planned protests in 15 countries around the world.
The use of the Internet to mobilize protesters in Russia is a new phenomenon.
"I used to express my opinion in my blog, in social networks, I wasn't really politically active," said Artyom Goryachev, a 27-year-old PR manager. "But enough is enough. I am fed up with all of this."
He said he planned to go to Saturday's protest with friends from work.
Anton Nossik, a popular blogger and Internet expert, said it was not the Internet that energized the protesters but the brazen vote rigging that prompted many young Russians to express their discontent offline.
"They came out not because they read information [online] on where to show up for the first time, but because for the first time many people got the feeling that the time had come for that," Nossik said.
Sam Greene, director of the Center for the Study of New Media and Society in Moscow, said this week's protests in Moscow were a combination of online and offline social networks working together.
"They're going out to protests with people they know, with people they trust," he said.
The Internet doesn't create protests or a revolution, "but it certainly makes it possible for people to communicate and to learn about what's going on around them in an environment like Russia, where the traditional media are much more closely controlled," Greene said.
Russia's Kremlin-controlled television networks have largely ignored the demonstrations.
Mansur Mirovalev, Jim Heintz and Sofia Javed in Moscow, Slobodan Lekic in Brussels and Maria Danilova in Kiev, Ukraine, contributed to this report.