Auxiliary Bishop P. Francis Murphy of Baltimore challenged the Roman Catholic National Assembly of Religious Brothers, which met here last weekend, to follow the lead of American Catholic bishops in their efforts to promote peace.

Murphy, a strong supporter of the American hierarchy's landmark pastoral letter condemning nuclear warfare, said that Catholics, in their peace efforts, must surmount old stereotypes that in the past have linked the church closely with national policy.

"If we are to address seriously the nuclear threat and the cultural crisis it manifests, we need to face our own history of moral accommodation," he said, noting that Catholics have "generally conformed to the patterns of American values and practices" throughout the nation's history.

Catholics must move from "our own history of moral accommodation" in the past and "clarify and assert our traditional moral principles" in the light of the present day world crises, he said.

"We are called to re-assess the church's relationship to the modern world and to determine the best manner in which the church can structure its political presence within the modern state."

Murphy made his comments during a peace vigil near the LincolnMemorial last Saturday evening. The vigil honored a variety of contemporary peacemakers, from Martin Luther King Jr. to present-day missionaries in Latin America.

The bishops' pastoral on peace has placed the American hierarchy "closer than ever before to a direct confrontation with our government over defense and foreign policies," Murphy said. The widely debated document, which was sharply criticized by the White House last November, challenges the morality of much of the Reagan administration's national defense policy.

"In the pastoral letter, as well as in previous statements of the United States Catholic Conference, we have recognized grave discrepancies between the foreign and defense policies of the United States and the requirement for world peace," Murphy said. "The significance of the pastoral for the future development of American Catholic social thought will depend upon our capacity to sustain active pursuit of the implications of our criticism."

In business sessions, the religious brothers expressed concern over the handling of the controversy involving Mary Agnes Mansour. The former Sister of Mercy nun was forced to resign from her order when she accepted a position as director of the Michigan Social Service Department, which administers Medicaid funding for abortions.

The brothers called on church leaders to develop a process for handling such controversies "that respects the principles of due process."