Freshly released CIA documents on the Bay of Pigs invasion provide new details on the confusion, mixed messages and last-minute changes in plans that ultimately doomed the mission.

The documents also underscore the extremes the United States went to maintain “plausible denial’’ of Washington’s role in the April 1961 invasion by CIA-trained Cuban exiles.

“These documents go to the heart of the historical debate over the Bay of Pigs — the issue of plausible denial,’’ said Peter Kornbluh, senior analyst at the National Security Archive, a Washington-based nonprofit research organization that had sought the documents for years and was instrumental in gaining their release.

Concerned that Washington’s hands could be traced to the invasion, the Kennedy administration kept scaling it back, said Kornbluh. It cut back on planned air raids on Cuban airfields and insisted on a problematic night-time landing of the invasion force.

The result: the defeat of the exile brigade in less than 72 hours, 114 men killed and another 1,100 captured.

Previously released documents show that while Kennedy never abandoned the notion that the Bay of Pigs invasion should remain covert, planners of the operations had begun to have their doubts about the operation’s success as a secret mission at least five months before the April invasion.

The declassified documents are among a set of five volumes on the invasion prepared by Jack Pfeiffer, a CIA historian who died in 1997.

Among the revelations:

•  Grayston Lynch, a CIA operative who had helped mark Playa Giron for the landing of Brigade 2506, reported an instance of friendly fire. After marking the beach, Lynch returned to the Blagar, a U.S. transport boat that was under attack by Cuban aircraft off and on until late on the afternoon of April 17.

The Blagar was equipped with eleven .50 caliber machine guns and two 75 mm recoilless rifles but because the U.S. planes had been painted with the insignia of Cuban aircraft, Lynch and the exiles aboard were having trouble distinguishing their targets.

“We sent a message very early on the first morning… [asking] those planes to stay away from us, because we couldn’t tell them from the Castro planes,’’ according to Lynch’s account. “We ended up shooting at two or three of them. We hit some of them there because when they came at us… it was a silhouette, that was all you could see.’’

The U.S. aircraft were supposed to be painted with blue stripes around the wings, Lynch said, but “they were impossible to see when they were coming at you.’’

Juan Clark, a paratrooper during the invasion and now a professor emeritus of sociology at Miami Dade College, remembers a green stripe on the underside of the U.S. planes.

“I had heard of friendly fire during the invasion,’’ he said Monday, “but not in that context.’’ Instead, he said, it was a Brigade combatant injured by friendly fire.

•  The CIA, with the support of the Pentagon, requested a series of large-scale sonic booms over Havana that would coincide with a preliminary air strike on April 14.

The rationale, according to Richard D. Drain, a top-level CIA invasion planner: “We were trying to create confusion and so on. I thought a sonic boom would be a helluva swell thing, you know…. Let’s see what it does…. Break all the windows in downtown Havana… distract Castro.’’