Much of the conflict is in two areas that, until now, have been nearly invisible to civilians: how the military hires its ministers and how they word their public prayers. Evangelical chaplains -- who are rising in numbers and clout amid a decline in Catholic priests and mainline Protestant ministers -- are challenging the status quo on both questions, causing even some evangelical commanders to worry about the impact on morale.

"There is a polarization that is beginning to set up that I don't think is helpful. Us versus them," said Air Force Col. Richard K. Hum, an Evangelical Free Church minister who is the executive director of the Armed Forces Chaplains Board. "I don't know whether it's an overflow of what's happening in society. But this sort of thing is so detrimental to what we are trying to do in the chaplaincy."

The Rev. MeLinda S. Morton, a Lutheran minister who resigned in June as an Air Force chaplain after criticizing the religious atmosphere at the Air Force Academy, said there has been a palpable rise in evangelical fervor not just among chaplains but also among the officer corps in general since she joined the military in 1982, originally as a launch officer in a nuclear missile silo.

"When we were coneheads -- missile officers -- I would never, ever have engaged in conversations with subordinates aligning my power and position as an officer with my views on faith matters," she said. Today, "I've heard of people being made incredibly uncomfortable by certain wing commanders who engage in sectarian devotions at staff meetings."

Diversity Without Quotas

The tradition of chaplains in the U.S. military goes back to George Washington, who first sought a minister for his Virginia regiment in 1756. In the early days of the republic, commanders simply chose a chaplain who shared their beliefs. But with the expansion of the military in World War II, the armed services set quotas for chaplains of various faiths, attempting to match the proportion of each denomination in the general population.

In a class-action lawsuit -- filed in 1999 in U.S. District Court for the District of Columbia and still in the discovery, or evidence-gathering, stage -- more than 50 Navy chaplains contend that the formula became a rigid and discriminatory "thirds rule": one-third Catholics, one-third mainline Protestants and one-third everybody else.

According to Hum, the military abandoned numerical targets about 20 years ago, partly for legal reasons and partly because the proliferation of religious groups made the system unworkable. Although chaplains are paid by the armed services, they must be ordained and "endorsed," or nominated, by religious organizations. The number of endorsers has grown from about 10 denominations in 1945 to more than 240 groups today, Hum said.

Like college admissions officers, Pentagon officials now say they seek diversity without using quotas.

"We don't actually say we want to have four rabbis this year, or 20 Catholic priests. What we do is, we look at who is sent to us by our endorsers throughout the country and . then we bring the best qualified into the chaplain corps," Rear Adm. Louis V. Iasiello, a Catholic priest and the chief of Navy chaplains, said in an interview at the Pentagon's Navy Annex.

Pentagon data analyzed by The Washington Post show a substantial rise in the number of evangelical chaplains in the past decade, along with a modest decline in mainline Protestant ministers and a precipitous drop in Catholic priests, mirroring a nationwide priest shortage.

Of the approximately 1.4 million people on active duty in the military, 21.5 percent list their religion as Roman Catholic. But of the 2,860 active-duty chaplains, 355 -- or 12.4 percent -- are Catholic priests.

By far the largest single provider of chaplains to the military is now the Southern Baptist Convention, with 451 chaplains, one for every 40 service members who list their denomination as Southern Baptist.

Although the military has had growing difficulty recruiting ministers from mainline Protestant seminaries, many evangelical denominations place a high priority on supplying chaplains to the military. The Church of God in Christ, for example, has 109 active-duty chaplains. The Full Gospel churches have 61, the Church of the Nazarene has 68, and the Cleveland, Tenn.-based Churches of God have 58.

The chief endorser of chaplains for the National Association of Evangelicals said he believes that the bias against evangelicals, though once real, is gone.

"When you look at the Navy today, you see evangelicals at the top of the hierarchy," said retired Col. Stephen W. Leonard, a former Army chaplain. He points to the deputy chief of Navy chaplains, Rear Adm. Robert F. Burt, who belongs to the Open Bible Standard Church, and to the previous chief of Navy chaplains, the Rev. Barry C. Black, a Seventh-day Adventist who became chaplain of the Senate after retiring from the Navy.

"There probably were chaplains that didn't get selected [for promotion] that probably should have been selected. But we're past that now. Let bygones be bygones," Leonard said.

How to Preach

With the growth in evangelicals, heated disputes are occurring over public prayers.

Iasiello said chaplains are free to preach however they wish in their base chapels or at sectarian worship services. But when they have a multi-faith audience at staff meetings, change-of-command ceremonies, ship commissionings and other public events, they are encouraged to offer more generic, inclusive prayers, he said.

"We train our people to be sensitive to the needs of all of God's people. We don't direct how a person's going to pray. Because everyone's own denomination or faith group has certain directives or certain ways of doing things, and we would never -- it's that whole separation-of-church-and-state thing -- we would never want to direct institutionally that a person could or couldn't do something," Iasiello said.

But the model of chaplaincy advocated by older chaplains such as Iasiello, which hinges on self-restraint, is increasingly under challenge by younger ones, such as Lt. Gordon James Klingenschmitt, 37.

Three years ago, Klingenschmitt left the Air Force, where he had been a missile officer for 11 years, and joined the Navy as a chaplain. He took a demotion and a pay cut to make the switch. But he was joyful.

"I had been serving my country," he said. "I wanted to serve God."

It was not long, however, before disillusionment set in. At the Navy Chaplains School in Newport, R.I., a senior military minister gave Klingenschmitt and other new chaplains a lesson in how to offer prayers in public settings. Classmates who prayed to a generic "God" or "Almighty" won praise. Those who prayed "in the name of Jesus" were counseled to be more sensitive, according to Klingenschmitt.

As a minister from a small evangelical denomination, the Evangelical Episcopal Church, Klingenschmitt bristled at those instructions. He wrote a paper citing a Pentagon regulation that "chaplains shall be permitted to conduct public worship according to the manner and forms of the church of which they are members."

Aboard the USS Anzio, his first post, he backed a Jewish sailor's request to receive kosher meals and tried to get permission for a Muslim crewman to take a turn offering the nightly benediction over the ship's public address system. But Klingenschmitt also insisted on his own right to preach what he believes as a born-again Christian.

In July 2004, he was reprimanded for a sermon at the memorial service of a sailor who died in a motorcycle accident. The sailor, Klingenschmitt said in a recent interview, was a Catholic, "and I had led him to a born-again experience before he died." In the sermon, he said, he emphasized that the sailor was certainly in heaven and "mentioned in passing" that according to John 3:36, those who do not accept Jesus are doomed for eternity.

"My sermon was in the base chapel, it was optional attendance, and it was by invitation. If we can't quote certain scriptures in the base chapel when people are invited to church, where can we quote them?" he said. "Don't paint me as a person who's going around forcing my faith on people. I've never done that."

In March, Klingenschmitt's commander recommended against extending his tour in the Navy, writing that he has "demonstrated recurring confusion concerning a chaplain's role within a military organization."

Klingenschmitt has accused the Navy of religious discrimination, contending in a written complaint to his superiors that he was punished because he refused to practice a "government-sanitized" faith that he calls "Pluralism," with a capital P.

Navy officials declined to discuss Klingenschmitt's case. But they noted that the National Conference on Ministry to the Armed Forces, a private association to which most chaplains belong, says in its code of ethics that each chaplain must "function in a pluralistic environment" and "not proselytize from other religious bodies," though they "retain the right to evangelize those who are not affiliated."

Whether there should be any tacit limits on chaplains' free speech has also been an issue at the Air Force Academy. A team of observers from Yale Divinity School criticized one of the academy's ministers for urging Protestant cadets to tell their classmates that anyone who is "not born-again will burn in the fires of hell."

"Could there possibly be a worse time for this fundamentalist Christianity to be pushed in our military, when we're in a war and the people we are fighting are recruiting their members by saying we're Christian crusaders?" asked Mikey Weinstein, a 1977 Air Force Academy graduate and former Reagan White House official.

His complaints over the past 18 months about religious intolerance led to a Pentagon investigation in June that found "a lack of awareness over where the line is drawn between permissible and impermissible expression of beliefs."

Among other incidents, the academy commandant had urged cadets to use the "J for Jesus" hand signal with the thumb and index finger, the head football coach had told players that he expected to see them in church, and Jewish cadets had experienced anti-Semitic slurs after students were urged to see the Mel Gibson film "The Passion of the Christ."

Lt. Gen. Roger A. Brady, the Air Force's deputy chief of staff for personnel, assured a June 26 congressional hearing that "the clergy pretty much have the political correctness thing down" and that "most of the complaints are with cadets and cadet-led prayers." But Klingenschmitt, who has served in both the Navy and the Air Force, said he thinks they share a basic flaw.

In both services, he said, "the higher-ranking authorities can impose their faith on the junior authorities. It's just that in the Air Force they have more evangelicals in power, and in the Navy they have more pluralists in power."

Copyright 2005 The Washington Post Company