When the president of Baptist-run Baylor University received a complaint this spring that an R-rated movie had been shown on campus, he didn't dillydally.

First he suspended the student film society.

Then he blasted the complaining student.

Then he charged that a "religious KGB" of fundamentalist students was using "surveillance" techniques to poison the atmosphere of academic freedom on the nation's largest Baptist college campus.

Strong stuff, but these are parlous times at Baylor and for the 14-million-member Southern Baptist Convention, in which a "holy war" is raging between fundamentalists and moderates.

At issue is how literally the Bible should be interpreted. At stake are appointments to the boards of the seminaries, colleges and missions of the nation's largest Protestant denomination.

Fundamentalists have led the denomination for six years, and moderates fear that unless they can wrestle the presidency back at a showdown annual convention in Dallas next month, the fundamentalists will be able to use their appointive powers to institutionalize their control.

Baylor has become a kind of proxy war in the larger struggle. Though it is owned by the autonomous Baptist General Convention of Texas rather than by the full Southern Baptist Convention (SBC), it has been a thorn in the side of fundamentalists throughout the denomination.

"A lot of people see Baylor as the fair-haired boy of the moderates, so it's no surprise that fundamentalists have decided to take target practice on us," university chaplain W.J. Wimpee said.

The shooting began last year when Zig Ziglar, SBC vice president, blasted Baylor for employing a Spanish-language professor who is a Mormon (a religion that the SBC has categorized as a non-Christian "cult") and a religion professor who teaches that evolution is not incompatible with the Genesis account of creation.

It intensified in December, when a group of fundamentalist students issued a "student manifesto" that objected to the unsound doctrine being taught by religion department professors, to "pro-choice" speakers invited to participate in campus seminars, to R-rated movies shown by the student film society and to songs on the student union jukebox "that espoused immoral themes" such as Marvin Gaye's "Sexual Healing" and "Erotic City" by Prince.

Baylor President Herbert H. Reynolds said he believed that the authors of the manifesto were a "small but diligent" group working in league with SBC fundamentalists to discredit the university. But he also said he recognized that on matters of manners and mores, they had a point. Quietly, he saw to it that campus movies and jukebox songs would be more in keeping with Baptist standards.

So this spring, when the film society went ahead, over objections of its faculty sponsor and showed "If . . . ," a 1969 British boarding school farce containing nudity, profanity and homosexuality, Reynolds lowered the boom. He also issued his "religious KGB" broadside. Reaction on campus has been muted.

"Basically, the students have been sitting on the sidelines," said Paul McCoury, a leader of a moderate faction of students. "There are no more than two dozen fundamentalists on the campus of 11,000 students ."

By most measures, Baylor is weathering the storm. Alumni gifts are on the rise this year, and admission applications are up.

Still, there is considerable discomfort among religion faculty members who must "choose their words carefully, because everyone assumes that what he says in class is being secretly tape-recorded," said Dr. Glenn Hilburn, chairman of the department.

"We may have a tendency to give more interpretations than we did before, but when the time comes for a faculty member to state his beliefs, he still does," Hillburn added.

The religion department at Baylor, like many others around the country, has a rule against tape recording lectures to avoid having statements taken out of context. That doesn't stop students from taping.

Dr. Paige Patterson, president of the Criswell Center for Biblical Studies in Dallas and a leader of the fundamentalist faction, said he receives dozens of unsolicited tapes every year from seminary and college students who want to know if their professors have interpreted the Bible properly.

Patterson said he keeps an archive of such tapes but denied that it constitutes a "heresy file." He added that he found the antitaping rule curious.

"It suggests that their skirts are not clean," he said of the Baylor religion department. "They don't want these things taped. They don't want the people who are paying the bills to hear what they are saying."

Wimpee accused Patterson and others of "trying to tell us we are not Baptists because we don't go along with their literal interpretation of the Bible." He noted that the Baptist denomination was founded on the belief that every man is his own priest and every church is autonomous. The very heart of the religion, he said, is to respect diversity.

Some believe that a schism is inevitable. Others believe that this surge in doctrinal warfare, like others in the 140-year history of the SBC, will pass. Indeed, some see it as good for the SBC, one of the fastest-growing Protestant denominations in recent years.

"It's sort of like being awoken at night by the sound of a bunch of cats in a neighborhood fight," Patterson said. "You think to yourself that the howling is so bad there can't be possibly any cats left in the morning. Then you wake up and find that the only thing they made was more cats."