The Reagan administration yesterday shrugged off objections and complaints of "Califanoism" from conservative Sen. Jesse Helms (R-N.C.) and other tobacco-state legislators and endorsed legislation to place stronger health warning labels on cigarette packages.

Assistant Secretary for Health Edward N. Brandt Jr., flanked by the surgeon general and top cancer, heart and drug officials in the Department of Health and Human Services, told a House Commerce health subcommittee that the government believes using various warnings about specific risks of cigarettes would help "increase the public's knowledge of the hazards of smoking."

The government decision to support such legislation came despite recent warnings to HHS Secretary Richard S. Schweiker that antismoking efforts could create trouble for southern Republicans, much as the antismoking crusade of his predecessor, Joseph A. Califano Jr., caused political troubles for the Carter administration.

In letters obtained by The Washington Post, Helms complained about "what is perceived as incipient 'Califanoism' in your department," while freshman Rep. Eugene Johnston (R-N.C.) worried that antagonizing the tobacco industry could endanger election prospects for him and other "vulnerable" members of Congress.

Rep. L. H. Fountain (D-N.C.) also warned that more regulations would "injure the revenue bonanza which government receives from this honorable crop."

Johnston and Fountain cited an election pledge by President Reagan in September, 1980, saying that "my own Cabinet members will be far too busy with substantive matters to waste their time proselytizing against the dangers of cigarette smoking."

There were no indications yesterday that Schweiker has written back yet and HHS did not respond to a reporter's questions.

Sources did indicate that the go-ahead to generally endorse pending legislation to rotate the warning labels on cigarettes was made at the last minute by the Office of Management and Budget, apparently after special clearance from the White House. The decision came after HHS pushed for approval.

One government source called it a "victory over the political pressures being placed on the administration." Added another: "It was a cliffhanger." Earlier, sources said, some top personal aides to Schweiker had questioned "how far we wanted to go out front on this issue," but arguments about the health significance of cigarette smoking prevailed.

While Schweiker has not launched the kind of outspoken, personal campaign as did Califano, a reformed smoker, he has repeatedly stated his support for preventive health efforts. John Pinney, a Califano appointee who formerly headed the antismoking effort, noted that "in view of the administration's general philosophy. . . I think the secretary has taken a strong and commendable stance on the smoking issue."

Schweiker wrote the Federal Trade Commission late last year that "smoking is the chief preventable cause of death in our society," saying he was "committed to effective action to reduce cigarette-related disease and death."

In February, Surgeon General C. Everett Koop and Assistant Secretary Brandt released a strongly worded annual report on the cancer risks associated with smoking that was described as the government's "most serious indictment" of smoking ever.

But yesterday's testimony was the first to indicate how far the government is willing to go in supporting specific actions. Brandt said that such legislation was a "high priority" of the administration.

A bill introduced with 50 cosponors by Rep. Henry A. Waxman (D-Calif.), the health subcommittee chairman, would replace the current cigarette label--"cigarette smoking is dangerous to your health"--with rotating warnings. A similiar bill is sponsored by Sen. Orrin G. Hatch (R-Utah).

Five versions would warn against specific dangers, including the risks of heart disease, cancer and emphysema, the hazards to unborn children of pregnant women who smoke, and the benefits of quitting, no matter how long a person has smoked.

Brandt indicated that the administration was in general agreement with this approach, but believed that the warnings should simultaneously appear on different brands so that smokers would be "constantly exposed" to a wide variety of information.

He also said that the HHS secretary should have the flexibility to write the warnings rather than mandating them by law.

The legislation has alarmed cigarette manufacturers, who are expected to testify today that it is a punitive measure that would ultimately lead toward the prohibition of smoking. A Tobacco Institute spokesman said yesterday that the bill is "unsound scientifically."

But passage of the new smoking bills has become a top priority of major voluntary health organizations, including the American Cancer Society, American Heart Association, and the American Lung Association.