The U.S. State Department said on Wednesday that Moscow's decision to end the USAID activities in Russia was "regrettable".

"It is regrettable that Russia has taken this decision," State Department spokeswoman Victoria Nuland told reporters at a regular briefing.

Russia confirmed Wednesday that the United States Agency for International Development (USAID), the primary U.S. official aid agency, will leave the country as of Oct. 1. Moscow accused the agency of trying to influence Russia's domestic political affairs.

"This decision (to shut down USAID) is made due to attempts of the agency to influence political processes, civil society institutions, and elections at various levels, through distribution of grants," Russian Foreign Ministry spokesman Alexander Lukashevich said on Wednesday.

Lukashevich cited "serious questions" that arose from USAID activities in Russia, "especially in the North Caucasus."

At the Wednesday briefing, Nuland dismissed such allegation.

"We completely reject the notion that our support for civil society, democracy, human rights in any way interferes with elections," she said.

Nuland's remarks marked a change of tone with her previous statement. During a briefing on Tuesday, when asked if she was disappointed by Russia's decision, Nuland said: "Obviously, this is a sovereign decision that any country makes."

USAID, founded in 1961, is America's primary government agency responsible for administering civilian foreign aid. The agency opened its office in Moscow in 1992, with some 60 Russians and 13 U.S. citizens working for it currently.

During the APEC summit early this month, Russian Foreign Minister Sergei Lavrov informed the U.S. Secretary of State Hillary Clinton that Moscow would ask USAID to leave the country shortly.

According to Nuland's remarks on Tuesday, the USAID has spent about 2.7 billion U.S. dollars in total in Russia since the end of the former Soviet Union and the agency's budget for Russia in fiscal year 2012 is about 50 million dollars.