The US Agency for International Development says it plans to leave Ecuador amid an impasse with the government, just six months after the agency was kicked out of Bolivia, in what analysts say is another sign of the waning US influence in the region.

In a letter to USAID partners in the country on Thursday, acting Mission Director Christopher Cushing said the decision to leave Ecuador comes “as a result of the Government of Ecuador’s decision to prohibit approval of new USAID assistance programs.”

Mr. Cushing said the agency had $32 million in aid scheduled for programs in coming years in Ecuador, according to the letter, a copy of which was obtained by The Christian Science Monitor. A USAID official confirmed the letter’s authenticity.

“The government of Ecuador recently informed USAID it could not execute any new assistance activities or extend existing activities pending negotiation of a new agreement governing bilateral assistance,” says the official, who spoke on the condition of anonymity because of sensitive negotiations with the Ecuadorean government.

USAID has tried unsuccessfully for the past two years to renegotiate its agreement with Ecuador, the official says. “We’ve been incurring significant costs for recently launched projects focused on environmental protection and civil society strengthening which have been unable to proceed,” the official says. “The cancellation was the only fiscally prudent option.”

The office is expected to close its doors September 2014.

USAID’s departure comes amid an increasingly acrimonious relationship with President Rafael Correa. The decision also marks the second time this year that the agency has been forced out of a South American country after Bolivia’s President Evo Morales ousted it in May.

“This is both another sign that relations between the US and Ecuador are in some ways continuing to deteriorate, but also that US influence in the region isn’t what it used to be," says Steve Striffler, a professor of Latin American studies at the University of New Orleans who studies Ecuador. "These countries are able to carve out independence from the US in a way they weren’t in the past.

“The idea they would have kicked out USAID 10 or 15 years ago is unimaginable," Mr. Striffler says.

The US government’s reputation in the region has taken a series of hits in recent months, with revelations that the National Security Agency (NSA) spied on the leaders of Brazil and Mexico. (Although Brazil later admitted it was spying on US diplomats as well).

The hunt for the man who leaked those NSA files, Edward Snowden, caused another embarrassment for the US when the plane carrying President Morales was grounded in Vienna amid suspicions Mr. Snowden was aboard. The incident caused outrage in Latin America, with the Organization of American States condemning it and backing Morales.

'Independent and sovereign'

President Correa has made no secret of his disdain for US officials who he sees as overreaching their diplomatic duties and meddling in domestic affairs. In 2011, he kicked out the US ambassador for comments made in a diplomatic cable published by WikiLeaks that said Correa might have been aware of high-level police corruption.

A year later, he granted asylum to the face of WikiLeaks, Julian Assange, who is still holed up in Ecuador’s London embassy.

“In some ways these actions, and the [USAID decision] can be put in there too, are intended to say that we are an independent sovereign nation,” Striffler says. “In the perspective of many in Latin America, and with good reason, USAID is seen as an agent of US imperialism.”

Last year, Correa ordered his government to analyze the impact of a USAID exodus. Requests for comment to Ecuador’s Foreign Affairs Ministry were not returned Friday.

Correa in June was granted wide-ranging powers to intervene in the operations of non-governmental organizations (NGOs), which often receive funding from USAID. The decree also created a screening process for international groups wanting to work in the country.

In early December, the government shut down environmental NGO Fundación Pachamama after it was alleged that the group disrupted public peace while protesting oil drilling in the Amazon region. Pachamama was not receiving USAID funding at the time of its closure, but still highlights worries felt by internationally-funded non-profits.

“It is an anxious time for NGOs and their donors in Ecuador. Over the past few years, the government has waged a steady campaign to discredit and dismantle activist NGOs,” says the employee of one NGO that works in the country. The employee asked to not be named because the NGO continues to work in Ecuador. “This is where donors like USAID have gotten themselves in trouble, by funding activist NGOs that are critical of the government and its policies.”

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USAID has worked in Ecuador for more than 60 years, granting more than $800 million in assistance during that time, the letter said.

Editor's note: A previous version of this story misstated Pachamama's relationship with USAID.