President Obama's efforts to engage Cuba and promote reform on the communist island may have been damaged Friday by federal charges against a former State Department intelligence analyst for allegedly spying for Cuba over a 30-year period.

Walter Kendall Myers and his wife are accused of using grocery carts among their array of tools to pass government secrets, according to an indictment unsealed Friday.

The arrest comes two months after the Obama administration acted to relax a trade embargo imposed on Cuba since 1962 and days after the Organization of American States revoked the island nation's 1962 suspension.

Some fear the arrest could erode congressional support for easing tensions with the communist nation.

"I think it might be too early to know but it can't good," said Ted Piccone, a senior fellow and deputy director for foreign policy at Brookings Institution, who knew Myers when he worked at the State Department.

"I think the timing is certainly bad," he said, noting how the OAS's decision to readmit Cuba led some U.S. lawmakers to express their strong disapproval of lifting sanctions on the island nation.

"This is only going to fuel the fire for those who are opposed to a closer relationship with Cuba," Piccone said. "I don't know if it's enough to put the brakes on it but I think it will slow it down." 

Sydney Weintraub, a Latin American analyst at the Center for Strategic and International Studies agreed but added, "The fact that Cuba has a spying mechanism, no one is surprised about that. Who the person is is surprising."

State Department officials say Myers had been under investigation for three years, since before he retired in 2007. He had access to highly sensitive material, officials said.

Their methods of communicating with the Cubans included Morse code on shortwave radio, changing shopping carts at the grocery store and a face-to-face meeting with President Fidel Castro himself, court documents say.

Secretary of State Hillary Clinton has ordered a damage assessment of what the couple may have revealed.

David Kris, assistant attorney general for national security, described the couple's alleged spying for the communist government as "incredibly serious."

Philip Peters, a Cuba specialist and vice president of Lexington Institute, a public policy research center, said the arrests shouldn't stop Washington from pursuing diplomatic efforts with Havana.

"I think it's a fact of life, they have espionage against us and we do against them," he told FOXNews.com. But he added U.S. interests dictate renewing talks with Cuba.

"Just as we didn't stop negotiating arms control with the Soviet Union, our interests dictate we should engage with Cuba and that doesn't change because the spies were caught," he said.

The Associated Press contributed to this report.