The Federal Communications Commission ruled yesterday that government agencies may file complaints against broadcasters under the fairness doctrine, but rejected a Central Intelligence Agency complaint that ABC distorted the news when it aired a charge last September that the agency tried to have a U.S. businessman assassinated.

The CIA case was the first complaint ever filed by an arm of the federal government against a television network.

The commission's decision, which reconfirmed a staff decision in January, drew criticism from both sides.

"We believe that the FCC has violated the First Amendment by finding that government agencies are free to file fairness doctrine complaints," said Robert M. Gurss, a staff attorney for the Media Access Project, a public-interest communications law firm opposing the CIA's complaint.

"The fairness doctrine is properly used to help the public receive information, not as a government propaganda device," he said.

Michael McDonald, general counsel for the American Legal Foundation that filed the complaint along with the CIA, said that "the FCC has once again abdicated its authority to see that large news organizations do not engage in public deception of their audiences."

McDonald, who said the FCC staff in March had also dismissed a complaint by his public interest law firm against a CBS documentary concerning retired Army general William C. Westmoreland, called the commission "little more than a paper tiger."

The FCC said it voted against the CIA's complaint on the grounds that the agency did not furnish evidence from inside ABC, such as a document or tape, to show that the network deliberately intended to distort the news.

"Neither the CIA nor the American Legal Foundation provided any direct evidence that an ABC employe knew any element of the story was false," according to the FCC statement about the decision.

The CIA had tried to use the fairness doctrine to force ABC to retract allegations in a two-part series broadcast Sept. 19 and 20 that the agency had engaged in an array of illegal activities, including a plot to murder a businessman in Honolulu.

ABC later retracted the murder charge, but did not back away from the other allegations in the series.

The series, which was aired on ABC's "World News Tonight," concerned Ronald Ray Rewald, who faces federal criminal charges of fraud, tax evasion and perjury associated with the August 1983 collapse of his investment firm. In his defense, Rewald claimed he was a covert CIA agent and that the firm was set up and controlled by the agency.

The network also interviewed former prison guard Scott Barnes, who said he had been hired by the CIA to kill Rewald while he was in prison to keep the alleged CIA connection secret.

ABC reported on Nov. 21 that all its efforts to substantiate Barnes' claims had failed and that the network had "no reason to doubt the CIA's denials."

During yesterday's FCC meeting, however, Commissioner James H. Quello said the fact that ABC issued a retraction but not an apology was "very shoddy journalism. It bothers me . . . . "

Chairman Mark S. Fowler added later, "I think you have it quite right that there is a great majority of the press that simply is unable to get it right."

Fowler also said that the CIA deserves the same right to complain as "the Federal Reserve Board or the state of Hawaii or the Environmental Protection Agency."

"The CIA has not been and should not be accorded any special rights as a petitioner before this agency; neither should it be handicapped in any special way," he said.

The CIA was the first federal agency to use the FCC to complain about a news broadcast, McDonald said. He said the FCC's policy has been to depend not on "who files the complaint. Instead, they are issue-oriented."