Three liberal national unions have instructed their state affiliates in lowa to maintain an arm's-length distance from an effort to "draft" Sen. Edward M. Kennedy (D-Mass.) for the 1980 Democratic presidential nomination, dealing a severe blow to the movement in the state.

As a result, the top political operatives for unions representing communications workers and government employes have decided to boycott a meeting Saturday to launch the Kennedy effort. And one of the original spearheads of the session. Charles Gifford of the United Auto Workers, has been told he can attend the meeting, but only as an observer.

"If the word has come from on high that these unions are backing out of the coalition, it will substantially diminish the prospects for drafting Kennedy or anyone else in Iowa," said state Democratic Chairman Ed Campbell.

Iowa is considered crucial to President Carter. In 1976, it was the first place he demonstrated popular support and if he shows weakness there next year it could severly damage his reelection effort.

According to a recent poll by the Des Moines Register and Tribune, the president is favored by only 17 percent of Iowans, compared with 40 percent for Kennedy and 12 percent for California Gov. Edmund G. (Jerry) Brown Jr.

The loss of Gifford and the auto workers was considered particularly damaging to the pro-Kennedy campaign, which the Massachusetts senator has discouraged. Gifford was a key architect of Carter's startling victory in the 1976 Iowa caucuses, but he has since become disillusioned with the president:

Gifford could not be reached for comment. However, UAW spokesman Don Stillman said Gifford was told yesterday by union President Douglas Fraser that he could attend the strategy session, "but not as a dump-Carter partisan."

"Gifford is going to advance the policy that the UAW is neutral" at this stage of the 1980 race, Stillman said.

The Saturday meeting is sponsored by 17,000 Iowa members of the International Association of Machinists, who have vowed to launch an all-out drive to elect Kennedy delegates in the Iowa precinct caucuses next Jan. 21-the nation's first formal test of 1980 presidential candidates.

Iowa machinists' chief Bill Fenton expressed outrage that state labor leaders were being pressured to boycott the meeting. "I think it's a dark day for America when a top labor leader tells you you can't go to a political meeting," he said. "I don't understand it at all. I thought we lived in a democracy."

Fenton said he plans to go ahead with the Des Moines meeting, and expects from 50 to 100 persons to attend, including local union leaders. "What we're going to do is get a draft-Kennedy movement started," he said.

Two other key union leaders have received either direct or indirect instructions to stay away from the meeting. Doug Hart, area director of the American Federation of State, County and Municipal Employes, said he decided not to attend because his international union is still officially supporting Carter and "my presence might be interpreted as an endorsement of Kennedy." Herb Randels, of the Communications Workers of America, said he been told directly to stay away.

"It's not too smart to be starting this kind of movement this early," he said. "It causes problems in the party. We're going to have enough trouble in 1980 without having any bloodletting among ourselves."