A substantial number of American Roman Catholic bishops registered significant disagreement yesterday with the draft of a proposed pastoral letter condemning nuclear warfare.

But as the National Conference of Catholic Bishops began a private debate on the most controversial position paper the group has ever produced, it was not clear whether the majority wants it softened or toughened.

The bishops began their four-day annual meeting here by plunging immediately into consideration of the proposed pastoral letter that, in its current form, declares immoral any first-strike use of nuclear weapons and views a policy of nuclear deterrence as valid only when coupled with aggressive arms reduction negotiations.

Leaders of the hierarchy of almost 300 bishops, who are charged with the spiritual guidance of more than 50 million American Catholics, set the framework for the discussion by emphasizing the bishops' responsibility to deal with moral questions.

"At one level, the question of nuclear war is understood as an issue of politics or diplomacy," said Archbishop Joseph L. Bernardin of Chicago, chairman of the committee that drafted the 110-page statement on nuclear war.

But, he said, "because the nuclear issue is not simply political, but also a profoundly moral and religious question, the church must be a participant in the process of protecting the world and its people from the specter of nuclear destruction."

The conference president, Archbishop John R. Roach of St. Paul-Minneapolis, devoted his presidential address to a theological rationale for the proposed pastoral. He linked the bishops' pronouncement on the nuclear issue to their long battle against abortion and the right to life.

Denouncing "selective reverence for human life" as "a kind of contradiction in terms," he said the bishops must seek "to make reverence for human life a touchstone of our policy and practice in every context."

Differences among the bishops began to emerge in the opening debate when five bishops presented prepared statements of their views.

Most outspoken was Archbishop Philip Hannan of New Orleans, who wanted to scrap the entire statement and "substitute the messages of the Holy Father," Pope John Paul II, because the pastoral "has so many deficiencies," he said.

He faulted the proposed draft for its failure to sympathize "with the horrible suffering . . . of those enslaved by communism . . . . The arguments against the threat of using a nuclear weapon fail to mention the proportionality of the aggression and repression of the Reds."

Hannan also charged that the letter "ignores completely our duty to defend Western Europe," that it misrepresents the Reagan administration's arms reduction talks and that "issuance of this letter now would undercut our present negotiations."

At the other end, Archbishop Raymond G. Hunthausen of Seattle, an outspoken opponent of nuclear weaponry, wanted the final statement to "call on our people and government to begin to lay down our nuclear arms now, regardless of what others do," and to pledge church support, "materially and spiritually," for individuals who, like himself, practice civil disobedience to oppose the nuclear arms race.

Hunthausen, who has withheld a portion of his income tax to protest nuclear armament, got sustained applause from his fellow bishops.

Archbishop John R. Quinn of San Francisco asked that the statement clearly oppose deployment of the MX missile. President Reagan is scheduled to announce by Dec. 1 how the MX is to be based.

Reports from group discussions off-limits to everyone but the bishops indicated that many of the participants registered "significant differences" about how to handle the proposed document.

Bernardin, who has a reputation for reconciling opposing points of view, said that was to be expected at this point in the process. The document is to go through one, possibly two more revisions, based on bishops' criticisms, before being presented to the hierarchy for final action, probably at a specially called meeting next May in Chicago.

At that time, Bernardin said, "I hope we can come up with a document that will be acceptable to a large majority -- if not accepted, then respected."