By Jill Dougherty

Moscow warned that the Obama administration's support for democracy-building organizations in Russia is complicating relations between the two countries.

Russian Deputy Foreign Minister Sergei Ryabkov, in an interview with Interfax News Agency, said "This activity is reaching a scale that is turning into a problem in our relations."

"We really are concerned that Washington is funding certain groups and movements in Russia," Ryabkov said in the interview published Tuesday.

In December, as thousands of Russians marched in protest against election fraud, Prime Minister Vladimir Putin accused Secretary of State Hillary Clinton of giving a signal to the demonstrators to come into the streets.

The issue has picked up steam since March, and Putin's victory in the Russian presidential election.

The Obama administration is lobbying Congress to free $50 million to support nongovernmental organizations in Russia.

In an interview April 1 with CNN, Clinton defended the initiative. "We in the United States believe that every country would be better off if there were greater freedom of expression, freedom of religion, freedom of assembly," she told Foreign Affairs Correspondent Jill Dougherty, "because I think we represent that."

"I want the United States always to represent these values and to live them. And therefore, we're going to continue to promote them around the world."

At Tuesday's State Department briefing, spokeswoman Victoria Nuland said the fund is "designed to support a vibrant civil society in Russia and to allow us to work with those Russian NGOs who want to work with us, to develop their skills and their voice and their ability to represent the aspirations of Russians to increasingly deepen and strengthen their democracy."

But Moscow sees U.S. funding of democracy support groups as a continuation of so-called "color revolutions" that upended Moscow-friendly governments in Georgia in 2003 and Ukraine in 2004. Efforts to support the street protests in Moscow at the end of last year and in early 2012, some Russian officials charge, are an attempt to undermine the Russian government.

The heated comments come as the new U.S. ambassador to Russia, Michael McFaul, has run into a hornet's nest over the issue of human rights. McFaul, a former professor and author of books on the democracy movement in Russia, was recently featured in reports on a government-friendly television network vehemently defending his meeting with a well-known human rights activist as the reporter peppered him with questions.

The ambassador also accused the network of possibly hacking his e-mails and phone calls.

In the interview with CNN, Clinton brushed off Putin's personal criticism of her, saying she "was a little perplexed that I would be imputed such power that a mere signal, a mere word, would cause thousands of people to turn out."

"In fact," she said, "I think the demonstrators in the street got it right. They laughed at that. I mean, they knew why there were there. They want democracy, they want freedom, they want a voice in their affairs."