Former CIA agent Edwin P. Wilson was acquitted last night by a U.S. District Court jury here of conspiring in 1976 to murder a political opponent of Libyan ruler Muammar Qaddafi in what prosecutors said was a plot motivated by greed.

The verdict, reached after three hours of deliberation, was the first courtroom victory for Wilson, who had been convicted twice in recent months of smuggling arms and explosives to Libya under multimillion-dollar contracts with Qaddafi.

Wilson is serving prison sentences totalling 32 years on those convictions and has been ordered to pay $345,000 in fines. As last night's verdict was read, he turned silently to defense attorney Patrick M. Wall and shook his hand before being led away under heavy guard.

Wilson could have been sentenced to 10 years in prison and $11,000 in fines here if he had been convicted on the counts of murder conspiracy and conspiracy to solicit murder. He still faces a trial in New York on a charge of conspiring to assassinate two federal prosecutors and seven potential witnesses at a previous trial. He also faces a second trial in Washington on explosive-smuggling charges.

Assistant U.S. Attorney E. Lawrence Barcella Jr. said after the acquittal last night he was disappointed. Wall, a New York lawyer representing Wilson for the first time, said he regarded the charges against his client as a "tryable case that could have gone either way."

Prosecutors relied heavily during the four-day trial on a key witness, Raphael Quintero, a Cuban exile who testified Wilson and a codefendant, Francis E. Terpil, approached him in August 1976 about an overseas murder contract.

Terpil is still at large and believed living in the Mideast.

Quintero testified he recruited two fellow Cubans for the job because he was led to believe by Wilson and Terpil that the target of the alleged plot was the international terrorist "Carlos." When the three were told later the target was former Libyan minister of planning Umar Abdullah Muhayshi, a foe of Qaddafi living in exile in Egypt, Quintero said they refused to participate.

Quintero, a veteran of the CIA's 1961 Bay of Pigs invasion of Cuba, also testified he later reported the alleged plot to his former CIA case officer.

Under cross examination by Wall, Quintero said that it was Terpil, not Wilson, who was promoting the alleged murder scheme. Wilson appeared more interested in hiring one of the Cubans, Raoul Villaverde, as an explosives expert to train terrorists in Libya, Quintero testified.

Quintero also maintained, under Wall's questioning, that he could not recall two conversations in 1980 with a Washington lawyer, Kenneth E. Conklin, in which Conklin said Quintero denied telling prosecutors that a murder plot existed.

The third Cuban allegedly hired by Wilson and Terpil, Raoul Villaverde's brother Raphael, is dead. Prosecutor Barcella said last night that Raphael Villaverde would have been a major prosecution witness who could have testified as an eyewitness to two meetings at which Wilson and Terpil discussed the alleged plot.

In closing arguments yesterday, Wall depicted Quintero as a mercenary who was attracted to the alleged plot not by old ties to Wilson but by the $1 million fee Wilson allegedly offered for the killing.

Quintero's "job was to do what he was told," Wall asserted. "He'd kill on orders. I suggest to you, if he'd kill, he'd lie."

Quintero testified he had been recruited by Wilson to work for U.S. naval intelligence and was employed as an agent in 1976 when he was allegedly approached about the assassination plot.