WASHINGTON—Is the CIA covering up some dark secret about the assassination of John F. Kennedy?

Probably not. But you would not know it from the CIA's behavior.

For six years, the agency has fought to keep secret hundreds of documents from 1963, when an anti-Castro Cuban group it paid clashed publicly with the soon-to-be assassin, Lee Harvey Oswald. The CIA says it is only protecting legitimate secrets. But because of the agency's history of stonewalling assassination inquiries, even researchers with no use for conspiracy thinking question its stance.

The files in question, some released under direction of the court and hundreds more that are still secret, involve the curious career of George E. Joannides, the case officer who oversaw the dissident Cubans in 1963. In 1978, the agency made Joannides the liaison to the House Select Committee on Assassinations—but never told the committee of his earlier role.

That concealment has fueled suspicion that Joannides' real assignment was to limit what the House committee could learn about CIA activities. The agency's deception was first reported in 2001 by Jefferson Morley, a journalist and author who has doggedly pursued the files ever since, represented by James H. Lesar, a Washington lawyer specializing in Freedom of Information Act lawsuits.

“;The CIA's conduct is maddening,”; said Morley, 51, a former Washington Post reporter and author of a 2008 biography of a former CIA station chief in Mexico. After years of meticulous reporting on Joannides, who died at age 68 in 1990, he is convinced there is more to learn.

“;I know there's a story here,”; Morley said. “;The confirmation is that the CIA treats these documents as extremely sensitive.”;

Morley's quest has gained prominent supporters, including John R. Tunheim, a federal judge in Minnesota who served in 1994 and 1995 as chairman of the Assassination Records Review Board, created by Congress to unearth documents related to the case.

“;I think we were probably misled by the agency,”; Tunheim said, referring to the Joannides records. “;This material should be released.”;

Gerald Posner, author of an anti-conspiracy account of the JFK assassination, “;Case Closed,”; said the CIA's withholding such aged documents is “;a perfect example of why nobody trusts the agency.”;

“;It feeds the conspiracy theorists who say, 'You're hiding something,”;' Posner said.

After losing an appeals court decision in Mr. Morley's lawsuit, the CIA last year released material confirming Joannides' deep involvement with the anti-Castro Cubans who confronted Oswald. But the agency is withholding 295 specific documents from the 1960s and '70s, while refusing to confirm or deny the existence of many others, saying their release would cause “;extremely grave damage”; to national security.

“;The methods of defeating or deterring covert action in the 1960s and 1970s can still be instructive to the United States' current enemies,”; a CIA official wrote in a court filing.

An agency spokesman, Paul Gimigliano, said the CIA had opened all files relevant to the assassination to Tunheim's review board and denied that it is trying to avoid embarrassment. “;The record doesn't support that, any more than it supports conspiracy theories, offensive on their face, that the CIA had a hand in President Kennedy's death,”; Gimigliano said.

CIA secrecy has been hotly debated this year, with agency officials protesting the Obama administration's decision to release legal opinions describing brutal interrogation methods. House Speaker Nancy Pelosi came under attack from Republicans after she accused the CIA of misleading Congress about waterboarding, adding, “;They mislead us all the time.”;

On the Kennedy assassination, the deceptions began in 1964 with the Warren Commission. The CIA concealed its unsuccessful schemes to kill Fidel Castro and its ties to the anti-Castro DRE, the Directorio Revolucionario Estudantil, or Cuban Student Directorate, which got $50,000 a month in CIA support during 1963.

In August 1963, Oswald visited a New Orleans shop owned by a DRE official, feigning sympathy with the group's goal of overthrowing Castro. A few days later, DRE members found Oswald handing out pro-Castro pamphlets and got into a brawl with him. Later that month, Oswald debated the anti-Castro Cubans on a local radio station.

Morley's lawsuit has uncovered the central role in overseeing DRE activities of Joannides, deputy director of psychological warfare at the CIA's Miami station, code-named JM/WAVE. He worked closely with DRE leaders, documents show, corresponding with them under pseudonyms, paying their travel expenses and achieving an “;important degree of control”; over the group, as a July 1963 agency fitness report put it.

Fifteen years later, Joannides turned up again as the agency's representative to the House assassinations committee. Dan Hardway, then a law student working for the committee, recalled Joannides as “;a cold fish,”; thin and bespectacled, who firmly limited access to documents. Once, Hardway remembered, “;he handed me a thin file and just stood there. I blew up, and he said, 'This is all you're going to get.”;'

But neither Hardway nor the committee's staff director, G. Robert Blakey, had any idea that Joannides had played a role in the very anti-Castro activities from 1963 that the committee was scrutinizing.

When Morley first informed him about it a decade ago, Blakey was flabbergasted. “;If I'd known his role in 1963, I would have put Joannides under oath—he would have been a witness, not a facilitator,”; said Blakey, a law professor at Notre Dame. “;How do we know what he didn't give us?”;

After Oliver Stone's 1991 film “;J.F.K.”; fed wild speculation about the Kennedy case, Congress created the Assassination Records Review Board to release documents. But because the board, too, was not told of Joannides' 1963 work, they did not peruse his records, said Tunheim, the chairman.

“;If we'd known of his role in Miami in 1963, we would have pressed for all his records,”; said Tunheim. He said he may ask the current CIA director, Leon E. Panetta, to release the records, even if the names of people who are still alive must be redacted for privacy.

What motive could CIA officials have to bury the details of Joannides' work for so long? Did CIA officers or their Cuban contacts know more about Oswald than has been revealed? Or was the agency simply embarrassed by brushes with the future assassin—like the Dallas FBI officials who, after the assassination, destroyed a handwritten note Oswald had previously left for an FBI agent?

Or has Morley spent a decade on a wild goose chase?

Max Holland, who is writing a history of the Warren Commission, said the agency may be trying to preserve the principle of secrecy.

“;If you start going through the files of every CIA officer who had anything to do with anything that touched the assassination, that would have no end,”; Holland said

Posner, the anti-conspiracy author, said that if there really were something explosive involving the CIA and Kennedy, it wouldn't be in the files—not even in the documents the CIA has fought to keep secret.

“;Most conspiracy theorists don't understand this,”; Posner said. “;But if there really were a CIA plot, no documents would exist.”;