MOSCOW — Russia explained its decision to end the US Agency for International Development’s two decades of work in Russia by saying Wednesday that the agency was using its money to influence elections — a claim the United States denied.

The US State Department announced Tuesday that Russia has demanded USAID leave the country, a culmination of years of resentment about what Moscow sees as American interference aimed at undermining President Vladimir Putin’s hold on power.

‘‘We are talking about attempts through the issuing of grants to affect the course of political processes, including elections on various levels, and institutions of civil society,’’ said Foreign Ministry spokesman Alexander Lukashevich.

Nearly 60 percent of the aid agency’s $50 million annual budget this year has been allocated for the promotion of democracy and civil society in Russia. Some of this money has gone to support Russia’s only independent election monitoring group, Golos, which fielded thousands of observers in last winter’s elections and compiled reports of widespread vote fraud in support of Putin’s party.

Putin had accused Western governments of trying to influence the December parliamentary vote through grant recipients, and a state-owned television channel directly denounced Golos, showing suitcases full of dollars that the group supposedly had received. After those elections set off an unprecedented wave of protests, Putin accused the demonstrators of being paid by Washington.

The US State Department denied that it was trying to affect the outcome of elections.

‘‘We completely reject the notion that our support for civil society, democracy, human rights, in any way interferes with elections, whether in Russia or anywhere else in the world,’’ spokeswoman Victoria Nuland told reporters. ‘‘We do these programs all over the world.’’

Grigory Melkonyants, of Golos, said the expulsion of USAID was a logical extension of a Kremlin crackdown on dissent since Putin returned to the presidency in May.

‘‘All of this is part of a series of moves aimed at toughening policy toward protests, the Internet, NGOs, and freedom of speech,’’ he said. ‘‘The people who make these decisions intend to crack down on dissent and criticism in a way that is as harsh as possible. It is frightening even to think about what may happen tomorrow.’’