A new "Pastoral Letter on Peace and War" being prepared by America's Roman Catholic bishops challenges the U.S. strategy of nuclear deterrence and retaliation and questions whether Catholic servicemen can ethically take part in carrying out that strategy.

Although the proposed language in a draft of the letter is ambiguous, "there is no room for debate," one church source said, "that it raises questions for people who are sitting in missile silos or submarines."

The letter does not amount to an attempt to dictate religious marching orders to military personnel, church sources say, but rather is meant "to encourage Catholics and others to begin a process of moral reasoning about the ethical dimensions of modern military strategy and doctrine."

The document has stirred considerable debate between the National Conference of Catholic Bishops and the top levels of the Reagan administration, including lengthy letters of response to the draft letter from Secretary of Defense Caspar W. Weinberger and presidential national security adviser William P. Clark.

Although the draft letter reiterates some well-known church positions in opposition to nuclear war, it refines that opposition in specific ways and represents the first pastoral letter from American bishops that devotes itself exclusively to the issue of nuclear conflict and how to avoid it.

The raising of this issue by American bishops comes at a time when churches in West Germany, the Netherlands and Britain are also playing leading roles in opposition to nuclear policies and new weapons deployments, while supporting various freeze movements. The Reagan administration opposes these freeze movements, arguing that they will lock in place a current Soviet advantage in atomic arms and remove the incentive for Moscow to negotiate arms reductions.

The proposed pastoral letter, which in its first draft completed in June covered 66 pages, has been put together by a committee of five bishops headed by Archbishop Joseph L. Bernardin of Chicago.

A second draft, developed after studying more than 700 pages of comments and suggestions gathered in response to the first effort, will be distributed to the nation's 376 bishops next week and discussed when they meet here Nov. 15-18.

The contents of the second draft remain confidential until it is distributed, and church sources decline to say how the first draft has been modified. But they suggested that the portion of the first draft dealing with Catholic military personnel remains much the same.

In that first draft, the pastoral letter notes that "in this document, for example, we have spoken clearly against the deliberate use of weapons against civilian populations. Catholic military personnel must observe those prohibitions."

On the moral issues of nuclear strategy, the first draft says that "under no circumstances" may nuclear weapons be used against population centers or predominantly civilian targets or even against military targets that are close to populated areas.

This applies even if American cities are hit first, the bishops say, because striking back at innocent people serves "purely as an act of vengeance." The bishops condemn even the threat of using atomic weapons against populated areas.

Also ruled out is the first use of atomic weapons, a tactic that lies at the cornerstone of U.S.-NATO strategy to repel an invasion of Western Europe by Soviet forces. This policy has also been questioned recently by some former top U.S. officials.

The first draft does not advocate unilateral abandonment of atomic arms by the United States, acknowledging that this might invite attack. But the draft concludes that the bishops "find ourselves at odds with elements of current" U.S. strategy, which they call "a marginally justifiable deterrent policy."

Reacting to this assessment, White House adviser Clark said he was "troubled about what appears to be a fundamental misunderstanding" in the church letter about U.S. policy.

Clark said that to deter the Soviets it must be made clear that the United States has the capability to knock out another country's leadership, military forces and "that critical industrial capability which sustains war."

He said that "for moral, political and military reasons, it is not our policy to target Soviet civilian populations as such . . . . An understanding of this point appears to be seriously missing from the draft letter."

Clark adds that while "our targeting policy does not call for attack on cities per se, . . . no one should doubt that a general nuclear war would result in a high loss of human life."

Weinberger warned the bishops that, given the success of longstanding policies of nuclear deterrence, "the burden of proof must fall upon those who would depart" from them. He called the policy sketched in the pastoral letter "dangerous" and argued that deterrence of war "would not be enhanced by adopting policies which may suggest to an aggressor that aggression would not be countered by an appropriate and effective response."

Church sources would not say yesterday what effect, if any, the Clark and Weinberger letters had on preparation of the second draft.

The language of the first draft addresssing military personnel prompted an analysis in the current edition of the conservative magazine National Review that claimed "it would be the first time in U.S. history that a major church told its members in the military service to refuse to obey orders related to essential national defense."

Church sources reject that analysis as too harsh, saying the idea was to provide guidance for thinking about the issue rather than to issue orders.