FREMONT, Calif. – Two centuries ago, outside the walls of Mission San Jose, Spanish soldiers battled with roving bands of Indians intent on driving the Spanish out. Now, this mission and 20 others scattered from San Diego to Sonoma stand at the center of a new confrontation over the separation of church and state in modern-day America.

The looming legal fight is over funds to preserve and maintain the missions against a variety of perils, the most serious of which are the earthquakes that regularly rumble across this state, cracking the missions’ adobe walls. A December 2003 quake badly damaged Mission San Miguel, causing structural damage that has indefinitely closed the historic site to visitors.

In November 2004, President Bush signed a bill authorizing the expenditure of up to $10 million in federal funds to support upkeep and repair of the missions over the next five years. Just two days after the bill became law, four California residents, backed by Americans United for Separation of Church and State, filed a lawsuit to block the program.

The suit claims that directing federal money to the Catholic missions would violate the Constitution.

“We don’t believe that taxpayers ought to be asked to bail out any active religious community, and 19 of the 21 missions are still owned and operated fully by the Roman Catholic Church,” the executive director of Americans United, the Reverend Barry Lynn, said in an interview. “You shouldn’t be coming to the government to repair your roof.”

Rev. Lynn said federal funding for the missions would, in essence, put the government in the church-building business. “If you can repair a religious building, why not just build it from the start?” he asked.

The defendant in the lawsuit is the interior secretary, Gale Norton, whose department would oversee disbursement of the restoration money. However, more than half a dozen missions and related groups have asked for permission to intervene in the case.

“Preservation funds go to barns, as long as they’re 50 years old or older,”said an attorney representing the missions, Jared Leland of the Washington-based Becket Fund for Religious Liberty. “Federal financial assistance can go to barns, but not to historic California missions?” Mr. Leland asked.

The missions were built in the late 1700s and early 1800s as sanctuaries for Franciscan priests traveling through California. Native-American converts were housed at the missions, as were Spanish soldiers who fought pitched battles with Indians less receptive to the entreaties of the church. In the mid-1800s, many of the missions were “secularized” by the government. A few decades later, most of the buildings, often in considerable disrepair, were returned to the church.

Mr. Leland said that for decades the missions have been acknowledged to be a critical part of California’s history, as well as public school curricula. “Doing a project on the missions or seeing the missions is almost a right of passage in California,” he said.

“I like to call them California’s pyramids,” the president of the California Mission Foundation, Knox Mellon, said.

One of the individuals seeking to join the court fight on the side of the missions, Roger Stokes, said he is motivated purely by secular concerns.

“My whole religious affiliation has dropped away. It’s practically zero. I’m not coming at this from a religious

point of view, but from a historical point of view,” Mr. Stokes, 65, a retired investment banker and occasional substitute teacher, said.

Mr. Stokes said he has fond memories of a childhood trip to every one of California’s missions. “We didn’t do that as a religious pilgrimage. We did it as a historical pilgrimage,” he said.

Mr. Stokes said preserving the missions is hardly a public relations boon for the Catholic Church. He called the mission era “a dark part of the history of California” and noted that the Spanish sometimes used coercion and violence to win converts. “I’m a firm believer that we should see the entire story, both positive and negative. … I’m not carrying the flag for Indians or white men or Chinese or anybody else.”

Supporters of the funding for the missions say using public funds to pay for restoration of sites of both religious and historical significance is far from unprecedented. The Old North Church in Boston, the Touro Synagogue in Newport, R.I., and the Eldridge Street Synagogue in Manhattan have all received funds through a federal program known as Save America’s Treasures. The program was begun by Senator Clinton in 1998, when she was first lady. However, it was not until 2003 that a new legal opinion cleared the way for institutions to apply for the federal historic preservation money, according to a spokeswoman for the program, Erin Angell.

“They still have to meet the same requirements. They have to be open to the public; no discrimination. There was no reason to exclude them from bricks-and-mortar preservation funding,” Ms. Angell said.

The church-state separation advocate, Rev. Lynn, said the missions do not meet those criteria. One of the anonymous plaintiffs in the court challenge asserts that he was denied permission to hold his wedding in one of the missions because he is not Catholic.

Mr. Mellon, the Mission Foundation chief, confirmed that non-Catholics are usually barred from marrying in the main mission buildings, but he said they can usually do so on the grounds.

In Congress, the legislation drew support from both ends of the political spectrum. One of the key backers of the bill was one of the most liberal members of the Senate, Senator Boxer, a Democrat of California.

“She’s a Democrat of Jewish identification,” Mr. Mellon said. “Her position obviously is not religious.”

Asked about the senator’s position, Rev. Lynn said, “Senator Boxer understands church-state separation is a serious question. She just has a different view on this.”

Ms. Boxer’s office did not respond to a request for comment for this story.

The court case is pending in Washington before Judge Richard Leon, an appointee of Mr. Bush. The government has asked that the suit be thrown out as premature, because while the funding for the missions has been authorized by Congress, no money has been officially appropriated. Judge Leon has not acted on the motion.

Rev. Lynn scoffed at the notion that the missions should be immune from legal challenge because other religious institutions have won funds in the past. “It’s like, ‘We can go rob a bank because we’ve heard other banks were robbed and they didn’t get caught,'” he said.

He rejected the notion that his group is hostile to religious historical sites. He said the problem with funding the missions is that they are active church parishes, many of which celebrate mass daily. “If these were museums with religious art, we wouldn’t complain about that,” he added.

Rev. Lynn also suggested that if the Catholic Church wanted to refurbish the missions, it could. “The archdiocese of Los Angeles decided to spend. … $150 million to build a big new cathedral,” he said. “That’s a choice the church makes.”

Mr. Stokes, the preservation advocate, said he is baffled by the suggestion that the government should not be involved in restoring the missions. “You go to Israel and stand in front of a wall that’s 3,000 years old, and now we’re not going to support a building that’s been here 250 years?” he asked. “If you don’t take care of something, it will end up on the ground. … I’m very, very adamant about this.”