The nation's Roman Catholic bishops will not be "intimidated" by a White House complaint that they have misread administration policy in drafting their proposed pastoral letter condemning nuclear war, the chairman of the drafting committee said yesterday.

"Obviously there is a difference of opinion on a number of issues. We will see who is misreading whom," Archbishop Joseph L. Bernardin of Chicago said in response to the letter sent in President Reagan's behalf by White House national security adviser William P. Clark.

The bishop's proposed letter, now in its second draft, is a broadly worded denunciation of nuclear war. It condemns first use of nuclear weapons and their use against civilian targets, raises questions about the doctrine of deterrence and calls on both superpowers to reduce their nuclear armaments.

The administration tried after publication of the first draft last summer to soften some parts of the document, which will ultimately form the basis of the U.S. church's teachings on the subject. Administration officials were fearful the bishops' proposed pronouncement would strengthen the nuclear freeze movement in this country and said it might also weaken the U.S. bargaining position in arms talks with the Soviets.

In the new letter, Clark wrote that he was still dissatisfied in that "none of the serious U.S. arms control efforts, including major initiatives and ongoing U.S.-Soviet negotiations [are] described or even noted" in the second draft, which the bishops are now debating here.

"Your committee will surely recognize that the administration's nuclear reductions proposals clearly conform to the pastoral letter's recommendations for cuts in nuclear arsenals," he wrote.

He defended the policy of deterrence as well, saying its entire aim was prevention of nuclear war. "It is important for the Bishops Conference to know our decisions on nuclear armaments and our defense posture are guided by moral considerations as compelling as any which have faced mankind," he said. He also suggested the bishops were glossing over "the Soviet buildup which we face" and what he described as the injustice of the Soviet system.

Clark said the new draft of the bishops' letter reflected "fundamental misreadings" of administration policies, and chided the bishops for not making room in the document for "previous administration comments that were forwarded to you."

"We find the virtual omission of these perspectives puzzling," he said.

But Bernardin said the bishops had taken them into account. "We are not unfamiliar with the issues that have been raised," he remarked at his news conference.

However, he said the committee would take another look at the administration's criticisms when work begins on the third draft of the pastoral. "We are still in process," he said. "We still have a long way to go. The door is still open to new ideas."

In his letter, Clark appealed for the Catholic church's blessing on administration defense policies as an aid to U.S. arms limitation negotiations.

"I continue to believe that as the Bishops Conference reviews new drafts of the pastoral letter, a clear presentation of these [the administration's arms control] initiatives should lead to the Bishops Conference's strong support for them," Clark wrote.

He added that "such support would prove enormously helpful in making clear to the world America's seriousness in our efforts and would, in particular, add to Soviet incentives to agree to the reductions and verifiable limitations we are seeking."

The bishops will debate their proposed letter again today; then the drafting committee will come up with still another version. A final vote is not expected until next spring at the earliest.

Most other bishops willing to comment on the Clark letter indicated they too were undeterred by it. "They are saying what they think and we are going to say what we think," said Cardinal John Krol, of Philadelphia, who said he was "delighted" the White House reacted.

Bishop Raymond A. Lucker of New Ulm, Minn., challenged the administration's views on arms reduction. "They say they've made the effort, but we're not convinced, and it's not enough. It's rhetoric," he said, adding that the administration was really pushing for arms buildup rather than disarmament.

"We've known we are on very different wave lengths on the whole question," said Bishop Joseph F. Gossman of Raleigh, N.C.

At their session yesterday, the Catholic bishops received a note of encouragement from the bishops who head the second largest Protestant denomination in the country.

The Council of Bishops of the United Methodist Church, currently meeting in Birmingham, Ala., sent "warmest greetings" and "strong support" for the Catholic hierarchy's efforts. "We thank God for your courageous witness on behalf of peace with justice." The Methodist bishops adopted a similar, but shorter and less detailed, pastoral letter earlier this year.

With the resolution of their nuclear pastoral still at least six months away, the Catholic bishops yesterday laid the groundwork to take on another issue potentially as explosive: the role of women in the church.

A proposal by Bishop Michael McAuliffe of Jefferson City, Mo., for a church-wide study and "plan for pastoral action" on this issue met with wide support. The study, as projected by McAuliffe, will seek ways of expanding the role of women in the church in every area short of ordination to the priesthood, which has been precluded by papal decree.

The project is needed because "the women's movement is further advanced in the United States than anywhere else in the world," McAuliffe said. "As we talk about nuclear weapons as a special issue in the United States, so is the question of women special to the United States."