Comments made by US Secretary of State Hillary Clinton, in which she expressed "serious concerns" about the polls, acted as "a signal" for the Kremlin's critics, Putin said.
Speaking in Moscow on Thursday, the New York Times reported, Putin accused Clinton of being too hasty to judge the elections:
"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. They heard the signal and with the support of the US State Department began active work.”
Russia must "protect its sovereignty" against foreign governments' efforts to influence its home affairs, Putin continued, claiming that "hundreds of millions of dollars" from abroad had been spent to influence the election process.
He appeared to be referring to the Moscow-based Golos election watchdog, said news agency Ria Novosti. The organization faced pressure from the authorities ahead of the polls and was accused of accepting funding from groups affliated with the US government.
More from GlobalPost: Gorbachev: Russia must hold new elections
Putin warned that it would be necessary to consider "toughening responsiblity for those who take orders from foreign states to influence internal political processes."
Some of Russia's largest opposition rallies in years have been held in Moscow and St. Petersburg since Sunday's elections.
Thousands of people are expected to attend a protest this Saturday in Revolution Square, outside the walls of the Kremlin, according to social networking sites.
The authorities have given permission for the rally, but only if numbers are limited to 300 people, Ria Novosti said. The square was closed Thursday "for maintenance," Bloomberg reported.
Responding to Putin's comments, State Department spokesman Mark Toner said the US "would obviously support the rights of anyone to peaceful protest - emphasis on peaceful - anywhere in the world," including Russia.
Critics of Putin's United Russia allege that up to 25 percent of the party's votes were faked, according to the Moscow Times.
Electoral authorities say the polls were fair, and accuse activists of faking evidence to the contrary.
President Dmitry Medvedev nonetheless promised Thursday there would be an investigation into the allegations of fraud, Xinhua news agency reported.
More from GlobalPost: Troops on streets of Moscow to police post-election protests