MOSCOW — Prime Minister Vladimir V. Putin on Thursday accused Secretary of State Hillary Rodham Clinton of instigating protests over the results of Russia’s parliamentary elections by baselessly criticizing the vote as “dishonest and unfair” and he warned that Russia needed to protect against “interference” by foreign governments in its internal affairs.

Alexey Druzhinin/Agence France-Presse — Getty Images

Prime Minister Vladimir V. Putin of Russia spoke in Moscow on Thursday.

“I looked at the first reaction of our U.S. partners,” Mr. Putin said in remarks to political allies. “The first thing that the secretary of state did was say that they were not honest and not fair, but she had not even yet received the material from the observers.”
“She set the tone for some actors in our country and gave them a signal,” Mr. Putin continued. “They heard the signal, and with the support of the U.S. State Department, began active work.”
Mr. Putin’s remarks signaled a new worsening in relations with the United States, threatening the Obama administration’s efforts to “reset” the relationship with Russia. His critique was strikingly personal. By singling out Mrs. Clinton, rather than making a vague comment about the West, he effectively thrust the United States on the side of the protesters in the streets challenging the Kremlin’s authority, and not entirely without reason.
Mrs. Clinton has been outspoken in her criticism of the election, issuing several strongly worded statements, beginning on Monday, after a preliminary report was released by observers from the Organization for Security and Cooperation in Europe.
“The Russian people, like people everywhere, deserve the right to have their voices heard and their votes counted,” Mrs. Clinton said on Monday in Bonn, Germany, while attending a conference on Afghanistan that included Russia’s foreign minister, Sergey V. Lavrov.
“That means they deserve a free, fair, transparent election and leaders who are accountable to them,” she said.
The observers issued a scathing assessment in which they said their main concerns were deep structural problems, including the absence of separation between the government and United Russia, Mr. Putin’s party.
Petros Efthymiou, a coordinator of the observer mission, cited “the interference of the state in all levels of political life, the lack of necessary conditions for a fair competition and no independence of the media.”
Mrs. Clinton, asked about Mr. Putin’s remarks, reiterated her concerns at a NATO meeting in Brussels on Thursday. While stressing the importance of the relationship with Russia, she said, “At the same time, the United States and many others around the world have a strong commitment to democracy and human rights. It’s part of who we are. It’s our values. And we expressed concerns that we thought were well founded about the conduct of the election. We are supportive of the rights and aspirations of the Russian people to make progress and to realize a better future for themselves, and we hope to see that unfold in the years to come.”
Mr. Putin’s assertions of foreign meddling and his vow to protect Russian “sovereignty” came after three days in which the Russian government has moved forcefully to tamp down efforts to protest Sunday’s elections. The authorities arrested hundreds of demonstrators and deployed legions of pro-Kremlin young people in Moscow to occupy public squares and to chant, beat drums and drown out the opposition.

Another major opposition demonstration is being planned for Saturday in central Moscow, and while Mr. Putin said that lawful rallies should be permitted, his warnings about foreign interference suggested that the government would view the continuing protests over the elections as a threat and would take further steps to contain them.
“We have to protect our sovereignty, and it is necessary to think about improving the law and toughening responsibility for those who take orders from foreign states to influence internal political processes,” Mr. Putin said.
Speaking specifically about street demonstrations, he said, “If people act within the framework of the law, they should be entitled to express their opinion.” But he added, “If someone breaks the law, the authorities and law enforcement agencies need to demand that the law be followed, using any legal means.”
Large contingents of riot police remained in Moscow, as part of what officials have described as a period of heightened security around the elections.

The governing party, United Russia, which has nominated Mr. Putin for president, lost a surprising number of seats in Sunday’s elections. But opposition parties say those losses would have been even steeper were it not for the violations cited by election observers, including the brazen stuffing of ballot boxes at some polling stations.

And there were some predictions on Thursday that outrage over the election results would continue to grow.
“The protest mood is very widespread,” said Sergei A. Markov, a political analyst connected to the Kremlin and former member of Parliament with United Russia. “Especially in Moscow and Petersburg, people are broadly convinced that there was falsification.”
But Mr. Markov said that efforts to mobilize public opinion would have to battle against deeply entrenched skepticism that street protests will amount to much. “In Russia, people are strongly convinced that if there are protests, then nothing good will come out of them.”
Mr. Markov said he expected the government to treat the public like a whining child. “The authorities will attempt to conduct themselves with society as a parent would a child who is crying and demanding some kind of toy,” he said. “In this case, it is not correct to go out and buy the child a toy, but rather distract him with something else.
Mr. Putin’s accusations of foreign meddling could provide that distraction.
Government officials had previously accused Golos, the only independent election monitoring group in Russia, of being financed partly by the United States and other Western countries and of aiding foreign nations in meddling in Russia’s affairs.

At NATO headquarters in Brussels, Russia’s ambassador to the alliance, Dmitri O. Rogozin, echoed Mr. Putin’s remarks, saying the election was an internal matter for Russia and should not be subjected to criticism from Mrs. Clinton or others.
“This criticism of our election system in Russia by Hillary Clinton is very strange for us,” Mr. Rogozin said in an interview. “It is unacceptable.”
The election loomed over Thursday’s meeting between Russia and the alliance, already strained by disputes over missile defense and NATO’s operations in Libya and Afghanistan. Mr. Rogozin said that NATO’s leaders pledged to cooperate with Russia on military issues, while ignoring its basic concerns about an exit strategy in Afghanistan and the architecture of the missile defense system. “We want our position to be understood,” he said.

Tensions with NATO have been rising as Russia intensifies its complaints about the American missile defense system being deployed in Europe. American and NATO officials have sought to reassure Russia that the system is designed to counter threats from Iran, but the Russians say those assurances are not sufficient.
Mr. Lavrov reiterated Russia’s concerns in Brussels on Thursday. President Dmitri A. Medvedev has warned that Russia would respond to the deployment of the system — which is scheduled to be operational by next summer — with its own military deployments and that the dispute might even lead Russia to withdraw from the New Start arms control treaty.
A senior administration official traveling with Mrs. Clinton during her meetings at NATO said that the alliance would move ahead with the deployment regardless of Russia’s objections. The official said NATO officials considered Mr. Medvedev’s remarks to be largely rhetorical.
“This is something that was taking place within the context of the Russian elections,” the official said.
The political context will only get more complicated as Russia and the United States each look ahead to presidential elections in 2012.

Mr. Putin on Wednesday formally filed his registration papers as a candidate for president in elections to be held in March. In September, he announced his plans to return to the presidency — he served two terms as president before becoming prime minister.
The announcement that he would swap places with Mr. Medvedev seemed intended to help build support for United Russia in the parliamentary elections, but it seemed to have the opposite effect. The party, which had already been experiencing a decline in popularity, slipped further in the polls.
In Sunday’s elections, United Russia finished as the leading party, but with slightly less than 50 percent of the vote. In the new Parliament, it will control 238 seats, down from the 315 seats it now holds. The Communist Party finished second in the balloting, followed by Just Russia, a social democratic party, and the nationalist Liberal Democratic Party.