Ecuador's President Rafael Correa ordered 20 Pentagon officers and staff to leave the country, a US embassy official said.
Correa ordered the US Department of Defense personnel out of the country on April 7, said Jeffrey Weinshenker, a spokesman at the US embassy in Quito, Al-Alam reported.
In a statement released to AFP, Weinshenker said the United States respects Ecuador's right as a "sovereign" nation to expel the US military staff, but regrets that the move "will severely limit our bilateral cooperation on issues related to security".
The expulsions make good on a months-old threat by Correa to drastically pare back the presence of US military officers and staff in Ecuador, over concerns about US "espionage" and "American imperialism".
Quito in January said it wanted to reduce the number of US military staff on its territory, and also warned it would not allow US "espionage equipment" on its soil.
Correa said he became aware of what he described as a bloated US military presence in his country after learning that four Pentagon personnel were aboard an Ecuadoran military helicopter that came under fire in October near the border with Colombia.
Bilateral relations also have been strained by the controversy over US surveillance of foreign governments, which was brought to light by fugitive intelligence leaker Edward Snowden.
In 2009, Correa opted not to renew a lease that had allowed the United States to operate its counter-narcotics operation in South America.