A painted plastic baby Jesus, Mary, Joseph, wise men, angels, shepherds, camel, sheep, a donkey and a cow took their place in the straw of a 10-by-20 foot stable on the Ellipse yesterday, the first Nativity scene in 12 years to be part of the federal holiday display near the White House.

But the traditional Christian tableau, between the reindeer pens and the brick-lined pit for the Yule log fire, has fueled a small holy war. Several religious groups argue that the National Park Service's decision to include the creche in the federally sponsored Christmas Pageant of Peace is divisive and violates constitutional guarantees of separation of church and state.

"It is our firm belief that religious symbols of all faiths belong on religious and other private property, not on public property and not sponsored by the government," Christian and Jewish leaders said Monday in an unsuccessful appeal to Interior Secretary William P. Clark.

Sandra Alley, spokeswoman for the Park Service, said yesterday "the Secretary of Interior supports the National Park Service decision" to reinstate the creche in the annual observance.

A nativity scene had been part of the Pageant of Peace until 1973 when a U.S. district court of appeals said it violated First Amendment guarantees of church-state separation. But last March the Supreme Court, divided 5 to 4, ruled that a city-sponsored Christmas display in Pawtucket, R.I., could include a creche. That ruling, accompanied by pressure from fundamentalist Christian groups, prompted the Park Service to reinstate the nativity scene.

The 20-piece, slightly-less-than-life-size nativity scene, initially enclosed by a chain link fence, was donated by the private Pageant of Peace Committee Inc., the Park Service said. "There is no tax money involved," said Alley. "It will be maintained by the Pageant of Peace Committee. Legally, we feel we can do it."

David M. Gordis, executive vice president of the American Jewish Committee, said yesterday that "even if it is legal" -- a point he did not concede -- "we think it is bad public policy . . . . The very fact that you have to have a fence around it means that it polarizes rather than unites."

Late yesterday afternoon, the Park Service decided to replace the head-high fence that enclosed the creche with a lower one because the original barrier "gave the wrong impression," said spokesman Don Heileman.

Jewish groups have been in the forefront of opposition to the restoration of the creche in the national Christmas pageant, but Lutheran, Episcopal and Unitarian Universalist officials have also joined in protests.

Gordis said that his organization, one of the most influential in the Jewish community, views the creche controversy as one more "ominous" incident in recent years, "another crossing of the line" of church-state separation.

Add the government sponsorship of the creche to the push for prayers in public schools, the Reagan administration's "public display of religion," the portrayal of America as a Christian nation -- put all that together, said Gordis, "and that makes non-Christians feel like outsiders."

The Interfaith Conference, an organization of Catholic, Protestant, Jewish and Muslim communities in the nation's capital, side-stepped taking an explicit position on the nativity scene controversy. But the "seasonal message" issued by the group's executive committee, said in part, "It is unfortunate that there are those who would use these religious symbols to exalt only particular faith communities, and who would use their public prominence to describe an exclusivistic society that has no room for nonbelievers or believers of a different faith.