President Carter yesterday proposed that a special office be set up to protect civil servants who "blow the whistle" on government wrongdoing, but at the same time indicated that everyone who goes public would not necessarily qualify for such protection.

"The special counsel will be there, independent of me, to protect --through the courts, if necessary --those who are legitimate whistleblowers," Carter told a lunch gathering at the National Press Club.

But there is an "important. . . distinction to be drawn," the president said, between "legitimate whistleblowers" and persons like Frank W. Snepp, the ex-CIA agent who wrote a book, "Decent Interval," which is critical of the intelligence agency's role during the fall of Vietnam.

Carter said Snepp had the book published although he had "signed, voluntarily, a contract" with CIA Director Stansfield Turner that the book would be examined before publication "to assure there were no revelations of secret material."

"If everyone who came into the CIA or other highly secret organizations in government felt free to resign because of a dispute, or to retire at the end of satisfactory service and then write a book revealing our nation's utmost secrets, it would be very devastating to our nation's ability to protect ourselves in peace or war and to negotiate on a confidential and successful basis with other government leaders," Carter said.

He said Attorney General Griffin B. Bell has been looking into the matter because Bell "has decided that when a contract is signed, it ought to be honored."

Snepp, however, has accused Turner of an "outright lie" in claiming that there was a written contract with the agency to clear the book before publication.

A CIA spokesman has said that Snepp's promise to Turner was oral, not written, and that it was made in the presence of witnesses.

In any event Carter's "whistleblower" remarks yesterday did little to comfort people like A. Ernest Fitzgerald, who was fired in 1969 after revealing $2 billion in cost overruns associated with the Lockheed C5 cargo plane.

Fitzgerald sued successfully to get back his job as a cost-cutting expert for the Air Force. But he said yesterday that he is not allowed to look at major contracts and that he still faces hundreds thousands of dollars in legal fees as a result of the dispute.

"What's a 'legitimate' whistleblower?" Fitzgerald asked in an interview after Carter's remarks. "Are people like me 'legitimate'? It's the Justice Department that's fighting me right now," he said.

If Carter and other top officials want to help "whistleblowers" they should "come down like a ton of bricks" on those government agencies and officials "who do wrong," Fitzgerald said.

If they did that often enough, you wouldn't have any need for 'whistleblowers.' I don't believe you have to single out people just because they tell the truth. I would like to see telling the truth become normal behavior" in the federal bureaucracy, Fitzagerald said. "If that happened, we also wouldn't have any need for a special counsel. We could save the taxpayers a lot of money," he said.

More pointed remarks came from Dr. J. Anthony Morris, a former Federal Bureau of Biologics scientist who was fired in 1976 after criticizing the ill-fated swine flu innoculation program.