The Federal Trade Commission charged yesterday that R. J. Reynolds Tobacco Co. Inc. misled the public with an advertisement that the agency said downplayed the relationship between heart disease and smoking.

In an administrative complaint filed yesterday, the FTC said that the ad misrepresented the purpose and results of a government-funded research study by suggesting that the study tended to refute the theory that smoking causes heart disease and that the ad left out information that suggested a link between smoking and heart disease.

For instance, the ad failed to mention that men in the study who quit smoking had a significantly lower rate of coronary heart disease deaths than men who continued to smoke, according to the FTC.

The advertisement, titled "Of cigarettes and science," appeared in a number of major newspapers and magazines, including The Washington Post, The New York Times, Newsweek and Time, in March and June 1985.

The tobacco company, an RJR Nabisco Inc. subsidiary, accounts for about one-third of the cigarettes sold in the United States. R. J. Reynolds said it would challenge the FTC's action, labeling it an attack on free speech and the First Amendment.

The FTC voted 4 to 1 to issue the complaint. The agency's new chairman, Daniel Oliver, dissented. Oliver's arguments were similar to the company's.

"I believe that, as a matter of public policy, it is valuable for the public to hear all sides of an issue, and I am concerned about taking any action that may inhibit free expression of views that might not be popular to government regulators," he said.

"We at R. J. Reynolds do not claim this study proves that smoking doesn't cause heart disease," the ad stated. But it went on to say that "the controversy over smoking and health remains an open one."

The FTC said that the advertisement misled readers by suggesting that the study in question, the Multiple Risk Factor Intervention Trial, was designed and performed to test whether cigarette smoking causes coronary heart disease and that it provided credible scientific evidence that smoking is not as hazardous as the public or the reader had been led to believe.

The ad also failed to disclose that the results of the study "are consistent with previous studies showing that those who quit smoking enjoy a substantial decrease in coronary heart disease mortality," the FTC said.

If the complaint is upheld, the tobacco company could be barred from misrepresenting the results of the study or other research in future advertising or could be required to disclose the information about death from heart disease that the FTC said the advertising should have contained.

"The message in question was a fair and accurate commentary providing R. J. Reynolds Tobacco Co.'s opinion on one aspect of a significant public controversy: the smoking and health issue," a company spokesman said. The company has retained prominent First Amendment attorney Floyd Abrams to represent it in its challenge to the FTC action.

"The key issue at stake in this proceeding before the Federal Trade Commission is the right of a company to comment on important public matters," according to a statement prepared by Reynolds. "This proceeding by the FTC poses a serious threat to the freedom of speech of companies and individuals alike."

Abrams said that the Reynolds ad was similar to an editorial or an "op-ed" piece in a newspaper. "It was not a cigarette ad. It was an editorial ad," he said. "It seems to me a clear and unambiguous violation of the First Amendment for the FTC to commence this action. If the commission does not conclude that its complaint violates the First Amendment, the courts will."