A federal judge today threw out pretrial motions to dismiss charges against Jack Elder, Roman Catholic director of a Texas halfway house for Central American refugees. Elder is accused of driving three illegal Salvadoran aliens five miles from the shelter to a bus depot last March.

U.S. District Court Judge Hayden Head Jr. scheduled jury selection for Tuesday. Elder, 41, also scheduled for trial next month in Brownsville for allegedly driving Salvadorans from the Mexican border to the shelter, could be fined $9,000 and sentenced to 15 years in jail.

Head denied five motions, including one by Elder's attorneys that he was within his First Amendment right to "free exercise of religion" in giving three Salvadoran men a ride to the bus station in Harlingen.

Head had ruled Thursday that Elder acted out of deep religious convictions, but today he ruled that the American people's overriding interest in maintaining the integrity of U.S. borders outweighed Elder's First Amendment claim.

"Throughout the history of our country, immigration matters have been placed very high on the totem poles of the powers of the government," Head said, adding that courts have reserved to Congress the right to set immigration policy.

"Mr. Elder would assert that his assistance in the evasion of each alien's obligation to identify himself is a small and higher matter and that this court should look solely to conduct with respect to El Salvador, circumstances . . . that apparently are intolerable to many who flee the agonies of that country and that I, as judge, should not look at the rest of the world," Head said.

"The law does not require such a narrow view as proposed by the defendant. The United States is entitled to know who is crossing the borders," he said. Head urged Elder to aid Salvadoran refugees in "legitimate and lawful" ways, by helping those who reach U.S. soil to seek political asylum.

Attorneys for both sides declined to comment. "I'm going to be safe," Elder said. "No comment."

Before today's hearing, participants in the American Sanctuary Movement, born in March 1982 in an effort by church members to protect refugees from the Salvadoran civil war, had voiced optimism about Head's acceptance of Elder's religious convictions.

They said his ruling might give new life to the movement, 16 of whose members were named Jan. 10 in a 71-count federal indictment as co-conspirators to transport illegal aliens.

Head appeared to deflate those hopes this morning after Stephen Cooper, Elder's lead attorney, presented two immigration experts challenging the government's contention that freeing Elder would undermine an overloaded Immigration and Naturalization Service.

Cooper tried to call a specialist in refugee law to the stand to show, he said, that Salvadorans have been denied fair treatment in applying for asylum. Last year, according to the INS, 503 of 13,501 Salvadoran applications were granted.

Head intervened, saying, "I don't think that's relevant to any issue," and adding that Congress, not federal courts, is empowered to analyze such issues.

"How does your client's helping to evade the system further the congressional intent of immigration laws ?" Head asked. "You are arguing that Mr. Elder and the rest of the Sanctuary Movement be allowed to emigrate the 4.5 million people of El Salvador."

"Why can't someone of the Christian faith become equally concerned about death caused by disease?" he said. "Why does this court have to examine Mr. Elder's own definition to allow him to avoid this statute?"

Head also denied motions contending that Elder was selectively prosecuted, that he should not have been arrested because he acted within a common perception that transporting illegal aliens within the Rio Grande Valley is not illegal, that the statute is unconstitutionally vague and that pretrial testimony of the three Salvadorans should be suppressed because they identified Elder without a police lineup.

He previously ruled irrelevant a dismissal motion contending that Elder's actions fell under the purview of the Geneva convention and international refugee law.