The United States quickly dismissed the allegations as baseless, and said Bolivia's action showed it did not want good ties with Washington.
In a fiery speech to workers on May Day, the leftist president of South America's poorest country said the US Agency for International Development was in Bolivia "for political purposes, not social ones."
"No more USAID, which manipulates and uses our leaders," Morales said in the address in La Paz's Plaza de Armas.
Morales, a populist and Bolivia's first indigenous president, has been in power since 2006 and has followed a sometimes nationalist agenda hostile to Western governments and companies.
In 2008 he expelled the US ambassador and agents of the US Drug Enforcement Administration, accusing them of meddling in Bolivia's internal affairs.
Bolivia is a major producer of coca leaves, the raw material of cocaine.
During this previous crisis, the United States responded by expelling the Bolivian ambassador and ending trade privileges that it had granted Bolivia.
"With the government of the United States we have profound differences of an ideological, cultural and, especially, policy-related nature," Morales told the La Paz diplomatic corps last year.
"I hope that with the new framework agreement we can improve things, but I doubt it," he said.
US State Department spokesman Patrick Ventrell said today that all USAID had done in Bolivia was simply to try to help people live better. Washington deeply regrets the decision by Bolivia, he said.
After five years of efforts to normalise relations after the 2008 crisis, he said, "this action is a further demonstration that the Bolivian government is not interested in that vision."
The new US Secretary of State John Kerry had encouraged improved relations with Bolivia.
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