The nation's Roman Catholic bishops and the American Jewish Congress yesterday released an unprecedented agreement championing the rights of parents to make ultimate decisions regarding the treatment of handicapped newborns.

"Government ought not to intervene in medical decisions made by parents of handicapped children" without "a preponderance of evidence" that the rights of the children are in jeopardy, said the statement, entitled "Principles on Treatment of Handicapped Newborns."

But, the religious leaders warned, "Handicaps, in and of themselves, do not justify withholding of medical treatment when such treatment offers reasonable hope of benefit and does not impose excessive pain or other burdens on the patient."

The agreement is one of the most significant products of a continuing Catholic-Jewish dialogue that emerged out of the Second Vatican Council and is believed to be the first interfaith formulation on this increasingly complex life-and-death issue.

Set forth as six concise principles, the accord begins by affirming "the sanctity of human life," and that "Every newborn has the right to basic care: nurture, sustenance and relief from pain. In cases where parents are unable or unwilling to provide such care, our government should take all reasonable steps to do so."

Ethical and moral traditions of the Roman Catholic and Jewish faiths agree, the statement said, that "medical intervention" for handicapped newborns "is not required when such intervention is clearly futile andwould do no more than briefly prolong the act of dying."

The agreement was prompted in part by controversy over the 1982 "Baby Doe" case in Bloomington, Ind., according to the Rev. Edward M. Bryce, director of the National Conference of Catholic Bishops' Office of Pro-Life Activities here.

The Bloomington case involved a baby boy born with cardiac defects and Down's syndrome and without passageways to or from his stomach. His parents, with the support of their doctor, decided against surgery to construct an esophagus for the child. The infant was sedated and died of starvation at six days old, but not before he became a cause celebre, as other medical personnel and right-to-life groups fought to overturn the parents' decision.

The Catholic-Jewish statement asserts that when medical experts disagree on treatment of a life-threatening condition, parents must make "conscientious and medically informed choices," based on what "seems most likely to promote their child's best interest."

Both Bryce and Michael Wyschogrod of the American Jewish Congress' Institute of Jewish-Christian Relations, the two leaders in developing the statement, said they had too little information on the Baby Doe case to make a judgment on it.

But Bryce made it clear that his sympathies lie with those who sought to challenge the parents. "Here was a child that could have been treated -- where we have the technology to treat him -- and he was not treated," he said. Citing the doctors and nurses who opposed the parents' decision, Bryce said, "This was more than just sentimental people saying that boy didn't have to die."

Wyschogrod seemed to take the opposite position. Noting that the principles were "not designed to deal with specific cases," he said that generally, "I think the assumption has to be that parents are acting responsibly in the care of their children . . . We don't want the government routinely intervening in the judgment of parents."

Neither the principles nor a brief commentary accompanying them made any reference to the "quality of life" argument sometimes raised in discussions of severely handicapped children.

The commentary said that the anguishing decisions regarding handicapped infants must always put the child's welfare foremost. "What is best for the individual child should take precedence over any conflicting interests of parents or society."

The statement called for government aid for handicapped children "so that parents can make decisions about treatment without undue financial pressure."