The new draft of a controversial pastoral letter from the U.S. Roman Catholic bishops condemning the nuclear arms race has been made more "flexible" to accommodate the views of the Reagan administration and conservative clergymen who wanted to be tougher toward Moscow, the chairman of the drafting committee said yesterday.

The new version of the letter, the third, was released as Congress returned from its Easter recess to likely votes in the next several weeks on the Reagan defense budget, the MX missile and a nuclear freeze.

The draft, on which the bishops are scheduled to vote next month, softens somewhat language in the earlier versions that basically endorsed the nuclear freeze movement.

It is less emphatic than they were in opposition to new weapons such as the MX.

It puts fewer strictures on Catholics in the armed services and defense industries involved in nuclear activities.

It also devotes much more space to differences between U.S. and Soviet society and the "Soviet imperial drive for hegemony in regions of major strategic interest to that country."

But Cardinal Joseph Bernardin, archbishop of Chicago, told reporters at a news conference here that despite these changes "the document as a whole has not really lost its prophetic character or its basic moral thrust."

Bernardin is chairman of a committee of five bishops who have now produced three drafts in nine months of a letter "on war and peace" meant to provide "guidance for the Catholic conscience" on the moral issues of the nuclear age.

The first two drafts, published in June and November of last year, created major controversies. This was partly because they appeared just as the freeze and other anti-nuclear movements were gaining ground in this country and Europe. They seemed to endorse those movements and challenge major elements of administration policy.

Administration officials yesterday privately expressed satisfaction with some of the changes made in the new document, especially acceptance of a White House explanation of U.S. nuclear targeting policy.

One official said the White House felt the bishops had made "a genuine effort" to take the administration's views into account.

William P. Clark, Reagan's national security affairs adviser, said that "While we do not necessarily share all the bishops' specific judgments, we believe this document marks an important and reponsible contribution to the public discussion of the issue."

The 150-page draft, which will be debated at the National Conference of Catholic Bishops in Chicago May 2 and 3, continues to oppose some aspects of U.S. nuclear policy.

It continues to oppose starting a nuclear war under any circumstance. Thus the bishops oppose U.S. and NATO refusal to renounce "first use" of nuclear weapons if Europe is in danger of being overrun by conventional Soviet forces.

The new draft also urges "clear public resistance" to the idea that nuclear war is "winnable," that it is possible to survive such a war and thus reasonable to plan to fight "protracted nuclear wars." All these ideas cropped up in administration rhetoric in the first 18 months of Reagan's term.

The new draft notes that there can be a difference between rhetoric and real policy. "It is important to recognize," the new draft says, "that there has been substantial continuity in U.S. action policy in spite of real changes in declaratory policy."

This appeared to be a suggestion that Reagan administration policy may sound more fearsome than it is.

In a speech before the National Catholic Educational Association here yesterday, Bernardin urged that Catholics seize the present moment of nuclear debate to think hard and with "a certain freshness" about the horrors of nuclear war.

The bishops say a principal difference between the latest draft and earlier versions is that the new draft "makes it clear that not all statements in the letter have the same moral authority." Certain moral principles are binding but there are also specific applications and recommendations "upon which persons of good will may differ."

One such problem area has to do with nuclear deterrence. The new draft, like its predecessors, leaves room for deterrence. It offers a "strictly conditioned moral acceptance" of the deterrence idea--the threat of nuclear retaliation against any enemy who uses nuclear arms first.

There is a related problem, however: whether such retaliatory attacks can justifiably be targeted at civilian as well as military targets. Past drafts flatly condemned any attacks on civilians.

The new draft takes account of "clear" statements from Clark about U.S. targeting policy. Clark said that "for moral, political and military reasons, the United States does not target the Soviet civilian populations as such" but that it would be irresponsible to rule out hitting targets near civilians because that might lead the Soviets to shelter much of their "war-fighting" capability in cities.

But the draft points out that this raises further problems because there already are vast numbers of Soviet military targets in the vicinity of cities. Thus, the draft says, attacks on such targets still "could be deemed morally disproportionate" because of the many civilian casualties they would produce. The draft does not make a final judgment on that point, however.

The new draft supports immediate, bilateral, verifiable agreements to "curb" the testing, production and deployment of new nuclear weapons systems. This is generally supportive of the freeze movement, but stops short of last year's call for an immediate "halt" to such activities.

Similarly, last year the bishops emphasized that "we oppose" new potential first-strike weapons, and specifically mentioned the MX. Now, the MX is not mentioned and the draft says it is the church's position only to "resist" such weapons.

When reporters asked Bernardin how he would respond to charges that the committee had moved closer to Reagan administration policy, perhaps under pressure, he said that "admittedly, certain sections have been nuanced differently and there is a greater degree of flexibility" from earlier versions.

But he emphasized that the subject is "highly complex" and urged that the new draft "be looked at as a whole." He said the committee "has been very sensitive to comments made by this administration" as well as many other interests that were consulted. "We were in search of the truth, and that's why we heard so many people" and why the letter has gone through so many versions, he said.

He said the section on U.S.-Soviet relations had been expanded because some bishops felt the differences in the two societies had not been made clear enough.

So the new report emphasizes both Soviet military might and the lack of freedom and human rights in that society in contrast to the freedom of American bishops to produce such a controversial pastoral letter.

But the committee warns that "sensible and successful U.S. diplomacy . . . demands that we avoid the trap of a form of anti-Sovietism which fails to grasp the central danger of a superpower rivalry" in which both sides could blow each other up. The bishops strongly support nuclear arms control and acknowledge administration efforts in this field, but also call for "calculated risks" to break through existing stalemates and halt the arms race.