In the closing hours of its last session, Congress passed a bill establishing a National Historical Park around four of the Southwest's famous mission churches, thus fulfilling a 50-year dream of Texas conservationists.

President Carter signed the bill, which was attached as a rider to legislation funding Pennsylvania Avenue's redevelopment here.

But in a memorandum to Interior Secretary Cecil D. Andrus, Carter directed that no money be spent on the churches because it would be "inconsistent with church-state relationships."

The memo, which has caused a furor in Texas, raises broad questions about the National Park Service's relationship to the 70 churches within national parks. Many, such as Boston's Old North Church where Paul Revere's lanterns were placed, are of major historical significance.

The Nov. 17 memorandum, which originated in the Office of Management and Budget and caught Interior by surprise, has also become a political embarrassment. The administration had supported the park for two years and appears now to have suddenly changed course.

"This is a plain, unadulterated double-cross," charged San Antonio Archbishop Francis J. Furey, whose largely Mexican-American archdiocese includes the missions. "Many precedents already exist in the United States where active churches and synagogues have become a part of the preservation by the federal government of historic places."

William Whelan, the Park Service director, says the memorandum "has created one heck of lot of consternation. We're between a rock and a hard place. The law says one thing and the chief executive says another."

What particularly irks Furey and other Texas Catholics is Carter's directive in the memo that, "My administration will consider federal participation in the operation, maintenance, rehabilitation or restoration of the missions only if they cease being used as active parish churches and pass into secular ownership."

However, Whelan acknowledges "it would not be reasonable to expect the missions to be inactive. Those churches are right in the Mexican-American community and they are the centerpieces for a whole lifestyle."

Another administration official adds, half-facetiously, "We've assured them it's not a Southern Baptist plot to do in the Catholics, but there's some suspicion about it."

Whelan says the turnaround in support for the project was partly a result of its cost. The bill authorized up to $10 million for land acquisition around the missions and for restoration of the four churches which would remain the property of the archdiocese. But now the department estimates it would cost $30 million to $40 million which, Whelan said, amounts to a "blatant conflict of church and state."

The park service director, who met recently with the archbishop, said he hopes to find a "middle ground." However, Carter's memorandum specifically forbade Interior to appoint an advisory council, "or take other implementing steps without discussing it further with me." For the moment, the project is in limbo.

For the time being, the Interior Department is interpreting the Carter memo as "only relating to the San Antonio missions," Whelan said. But he added, "We don't know where this will lead."

Another Interior agency, the Heritage Conservation and Recreation Service, gives historical preservation grants to state projects, some of them active churches In the past four years, 167 churches have received about $2 million in federal funds.

The Park Service is currently negotiating an agreement to reimburse the Old North Church, an active Episcopal institution, for maintenance funds because of the many tourists who visit Boston's Freedom Trail, which the Park Service operates.

However, neither the Old North Church, nor any of the 36 government-owned churches and 34 privately owned churches in national parks have received funds approaching the amount contemplated by the Mission park bill, Whelan said.

For example, Park Service documents show that a methodist church in Cape Lookout National Seashore, in North Carolina, received $7,000 in 1978; a Catholic church in Grand Canyon National Park received $10,000; and a Catholic church at Philadelphia's Independence National Park received $8,000. All three churches hold religious services.

Asked if the churches could continue to hold services and receive federal aid after the president's memo, Interior spokesman Harmon Kallman said, "We're trying not to generalize this thing. The memo is principally concerned with this [San Antonio] project."

However, Sen. Lloyd Bentsen (D-Tex.), the archbishop and others, are raising the discrimination issue. Suggesting that the plan for the missions' operation was similar to that of Old North Church, Bentsen wrote Carter last month that the church-state issue was "fully considered and met in the drafting of the saw you signed...The very fact that these missions are active, living churches makes them all the more valuable as a bridge to a unique part of our nation's history."

The four missions, established by the Spaniards partly to Christianize the Indians and partly to defend the territory agaist the French, include San Jose, built in 1720 and Concepcion, San Juan Capistrano and Espada, dating to 1731. All are within a few miles of Texas' most famous mission, the Alamo.