REUTERS/Alejandro Ernesto
But the US Agency for International Development (USAID) did admit to building a Twitter-style application on which Cubans, who face strict curbs on expression, were able to "talk freely among themselves" consistent with universal rights and freedoms.
White House spokesman Jay Carney said the program was a "development assistance" scheme targeted at Cubans facing government restrictions on information and had never been a secret.
He said the program, first reported after an investigation by the Associated Press, was debated in Congress and conducted within US law. It was not advertised to protect those who took part.
"When you have a program like that in a non permissive environment, i.e. a place like Cuba, you are discreet (in) how you implement it so you protect the practitioners," he said.
"But that does not make it covert. USAID is a development agency, not an intelligence agency. Suggestions that this was a covert program are wrong."
USAID spokesman Matt Herrick said USAID was proud to work in Cuba to "promote human rights and universal freedoms" and to help information flow to its people, alongside its humanitarian operations.
The project was known as "Zunzuneo" after the term for a Cuban hummingbird and was a platform for Cubans to "speak freely among themselves," said Herrick.
He said the application was built to build interest among Cubans using topics like sports scores, weather, and trivia.
But questions were raised after the AP report suggested that political content was to be introduced at a later stage to encourage Cubans to mount "flash mobs" and demonstrate against the communist government.
Despite US the denials, the use of USAID in the program could politicize an agency which often relies on the goodwill of foreign governments to carry out humanitarian work.
Patrick Leahy, chairman of the Senate Judiciary Committee said he had not been briefed on the program, which he called "dumb, dumb, dumb."
"If you are going to do a covert program like this for regime change, assuming it ever makes any sense, it's not something that should be done through USAID," he said.
"They do a lot of great things around the world ... this is not one of them," Leahy told MSNBC.
The agency says openly on its website that its core mission in Cuba includes promoting the freedom of expression.
It says its program provides basic news and information about issues relevant to Cubans from "inside Cuba and around the world."
It uses books, magazines, newspapers, and pamphlets "with an increasing emphasis on promoting the use of social media."
Carney said Congress appropriated funds to promote democracy in Cuba in an open fashion and that the program had been vetted by the Government Accountability Office, a federal watchdog body.
State Department spokeswoman Marie Harf said that the purpose of the program was not to stir up pro-US sentiment in Cuba.
"We were trying to expand the space for Cubans to express themselves. They could have expressed anti-American views on it," she said.
"We weren't able to choose what they saw on these platforms. That's up to them."
Harf said $1.2 million was allocated for the program, which ended in 2012 when the contract ended. She said the program was not cancelled.
She also said Secretary of State John Kerry and his predecessor Hillary Clinton, a prospective 2016 presidential candidate, were not aware of its existence.
The confrontation between the United States and Cuba is one of the world's last Cold War-era disputes and Washington has maintained an embargo on the communist country since 1962.