With Aid Cutoff, Kremlin Recalibrates MOSCOW - It began as an urgent effort to stave off political chaos, build basic institutions, and even prevent starvation in the anxiety-ridden aftermath of the fall of the Soviet Union. Over the next 20 years, through the United States Agency for International Development, American taxpayers would come to spend nearly $3 billion on programs touching nearly every facet of society in the former Communist state - fighting the spread of tuberculosis and H.I.V., developing judicial systems and training lawyers and judges, promoting child welfare, job readiness, youth engagement, human rights and democracy, even helping modernize the electric grid. The decision by the Kremlin this month to terminate all the agency's programs here, amid a swirl of ominous accusations of meddling in Russia's internal affairs, has stunned aid workers, infuriated American diplomats and left many nonprofit groups on the brink of collapse. It also marks the end of an extraordinary collaboration between the two former cold war enemies, one that was unimpeded, at least initially, by the suspicion that often shadows foreign aid, in part because such programs have historically in many places provided cover for intelligence activities. "In the fall of 1991 and early in 1992, the door for Western engagement and influence in remaking the Russian economy and polity was wide open," Michael A. McFaul, the American ambassador, and his co-author, James M. Goldgeier, wrote in "Power and Purpose," a 2003 history of American policy after the cold war. Issues of sovereignty that often emerge as major sources of tension between donors and recipients in other countries were simply not an issue. They are now. With President Vladimir V. Putin facing the biggest political challenges since his rise to power 12 years ago, including an ongoing series of big street demonstrations in Moscow, the Kremlin has been moving aggressively to clamp down on dissent. When Mr. Putin last winter accused Secretary of State Hillary Rodham Clinton of sending "a signal" to opposition groups in Russia to take to the streets, many American officials dismissed it as election-year rhetoric, aimed at propping up his campaign for president. But the move to cancel long-established foreign aid programs, including many with no connection to politics, suggests that the fear of external influence is a deeper concern, and that an effort by Mr. Putin to recalibrate his relationship with the United States is under way. The Kremlin's ire seems largely directed at two groups: Golos, the country's only independent election monitoring organization, which helped expose fraud that favored the governing party in parliamentary elections last December; and Transparency International, an anticorruption group, which for a while seemed to have a good working relationship with former President Dmitri A. Medvedev. Russian officials insist that the United States should not have been surprised by their decision. "We have long warned the U.S. side that we are not satisfied with some aspects of U.S.A.I.D., in particular political aspects," said Aleksei Pushkov, the chairman of the foreign affairs committee in Parliament. Aleksandr Lukashevich, a spokesman for the Russian Foreign Ministry, said there were "serious questions" about the agency's work in Russia, including "attempts to influence the political process through the distribution of grants." Aid programs sometimes have ulterior motives. In their book, Mr. McFaul and Mr. Goldgeier described how American officials in the 1990s directed food aid to some areas in Russia that had been off-limits in Soviet times to get a look at those places. Still, leaders of the nonprofit groups active in the political arena reject the allegations that they are puppets of the West, and say their efforts are driven by a desire to fix problems in Russia. "It's hysterics and a nervous reaction from the government," said Grigory A. Melkonyants, the deputy director of Golos. It's useful for the government to blame the daily problems in Russia that we all see on NGOs. Critics of the cancellation of aid programs say the Russian government's anger is misdirected. "It is difficult to say what result is expected in the Kremlin from the closure of Russian U.S.A.I.D. programs," Maria Eismont wrote in a column in the daily newspaper Vedmosti. The protest movement is not going anywhere because people are not put on the streets by the State Department but by election fraud, the degradation of law enforcement and the judicial system, lack of a coherent social and migration policy, the collapse of health and education services and total disregard for citizens demonstrated by officials. Shutting down the international development agency in Russia may deal little more than a short-term setback, at least for the groups that have become political foes of the Kremlin; many of them have other sources of financing. Some groups, including Golos, already receive American aid through channels other than the agency, including the National Endowment for Democracy, a private group that receives financing from Congress. American officials have said they are working to find ways around Russia's decision, including the possibility of endowing a private foundation set up within Russia under Russian law. But many nonprofit programs stand to be devastated. Dmitry Goliaev, the director of the Russian Health Care Foundation, which employs 30 people in its fight against tuberculosis and H.I.V., said the group would be forced to stop work. "I am not going to assess every sector of U.S.A.I.D."s work," he said, "but I am convinced that its work in the health care sector responds to an acute need for Russia." Paige Alexander, the assistant administrator for Europe and Eurasia at the development agency, said the Kremlin's decision would only hurt its own citizens. "We have always been doing this from the American people to the Russian people," she said. And that's who is losing out. Andrew Roth, Anna Kordunsky and Ellen Barry contributed reporting.