The National Conference of Catholic Bishops begins its annual meeting here today amid pressure ranging from prayer vigils to secret diplomatic missions at the Vatican, all directed at influencing the bishops' proposed pastoral letter condemning nuclear warfare.

The conference is expected to devote almost half its four-day meeting at the Capital Hilton Hotel to the nuclear issue.

Newly formed organizations of conservative lay Catholics have mounted a campaign to leave foreign affairs to the professionals. On the other side, Catholic peaceniks are urging the bishops to take an even tougher stand.

". . . Bishops do their best work in the cathedral, not at the Pentagon," said Philip F. Lawler, director of studies at the conservative Heritage Foundation and president of the Catholic Center for Renewal.

The center, which Lawler said was chartered earlier this year but has "not been active until now," has hired a public relations firm that is blitzing the media with opposition to the bishops' stand against nuclear war.

Lawler maintains that the bishops should limit their involvement to exhorting "their followers to prayer and reflection on the issue."

Last month, another of the new lay Catholic conservative organizations, the American Catholic Committee, held a day-long conference here stressing the importance of a strong nuclear deterrence policy. The bishops' statement holds that nuclear deterrence is morally tolerable only if coupled with aggressive efforts at arms reduction agreements with the Soviet Union.

The American Catholic Committee has mailed every bishop a copy of a book containing speeches presented at that meeting, including remarks by Richard V. Allen, President Reagan's former national security adviser, and Frank Shakespeare, former director of the U.S. Information Agency.

New Yorker James McFadden, who said he founded the American Catholic Committee earlier this year, denied reports that his group has administration ties. "That couldn't be further from the truth," he said. "We have gotten no funds from the Reagan administration."

The preface to the organization's book says the American Catholic Committee was founded by "Catholic laymen concerned about the misinterpretation of Catholic teachings, especially on social and political issues."

The bishops' statement on nuclear warfare was drafted in early summer after more than a year of study and hearings involving experts from the government, military, ranks of theologians and the peace movement. Today the bishops will begin deliberations on a second draft, rewritten in light of criticism of the first.

Despite pressure from proponents, no final action is expected here. The bishops tentatively plan to meet in Chicago in May where a final vote is expected.

Archbishop John Roach of St. Paul-Minneapolis, head of the bishops conference, said he has "received nothing but encouragement" from the Vatican on the proposed pastoral letter. "I've felt no negative pressures," he said.

The bishops' deliberations have drawn worldwide attention. Reporters from Japan and a dozen European nations and from throughout the United States have received accreditation to cover the sessions.

Russell Shaw, the bishops' press officer, said the volume of inquiries from the media last week reminded him "of the week before the pope's visit" three years ago.

Objections raised by Defense Secretary Caspar W. Weinberger and presidential national security adviser William P. Clark failed to persuade the bishops to soften their condemnation of nuclear weapons in either first-strike or retaliatory situations.

Earlier this month, the administration acknowledged sending ambassador-at-large Vernon E. Walters to the Vatican, reportedly to try to persuade Pope John Paul II to influence the bishops to soften their stand. In fact, the Vatican was apprised of the statement and, according to church leaders here, is in sympathy with it.

While the bishops, because of the large numbers of American Catholics they represent, are receiving the most scrutiny for their wrestling with the nuclear issue, they are not alone among Christian church leaders in confronting the issue.

A similar report, to be debated by the Church of England in February, calls on Britain to abandon its reliance on nuclear deterrence. Its reception in Britain is comparable to the one accorded the Catholic bishops' report here.

Even before the bishops finish their sessions this week, American Baptists will gather at Calvary Baptist Church here for a national consultation on the same issue. At virtually every convention of a major Protestant denomination in the past two years, resolutions condemning the nuclear arms race have been overwhelmingly adopted.

"And this year, it was the lay delegates who were pushing the church leaders to be more aggressive," the Rev. Dr. Charles Bergstrom of the Lutheran Council said.