A high-ranking U.S. Roman Catholic Church delegation, including Washington Archbishop James A. Hickey, questioned Salvadoran President Jose Napoleon Duarte today on human rights issues and the use of U.S. military and economic aid here, the group's leader said.

Duarte urged the U.S. church "very frankly" to support continued U.S. aid to El Salvador to help "contain" problems here, New York Archbishop John J. O'Connor said in a statement after the meeting of more than two hours.

Before the meeting, Hickey lauded Duarte but said that the delegation was concerned that U.S. military aid could be used to violate human rights here. Afterward Hickey said briefly that the talks were "substantial" and "very useful."

O'Connor's statement did not spell out what the U.S. clerics told Duarte. The U.S. group has been careful to say that this is a "pastoral" visit designed to gather information and not to intervene in Salvadoran affairs.

But O'Connor said, "Naturally we were quite interested in the questions of military and economic assistance granted by the United States or withheld by the United States in some instances" because of human rights concerns.

He also said that the delegation spent "a fair amount of time" discussing the government's investigations of the killings of four U.S. churchwomen in December 1980. He added that the killings of two U.S. land reform advisers in January 1981 and of San Salvador's archbishop in March 1980 also were discussed. Little progress has been achieved in these inquiries since the conviction last spring of five National Guardsmen for killing the U.S. churchwomen.

For his part, Duarte "urged us very frankly that we support some level of continuing assistance to El Salvador because he felt that this would help nationalize, help contain the problems here, help humanize, and that a loss of support at this time could have a significantly adverse effect," O'Connor said.

Washington Archbishop Hickey, who knows Duarte personally, called the president "a dedicated, principled gentleman" who has "a big job." He said that the church delegation was "delighted that the number of political killings has dropped since Duarte's inauguration in June. But Hickey, in an interview, added that the human rights issue was to be raised both with Duarte and in a planned meeting this evening with Defense Minister Carlos Vides Casanova.

"The whole question of human rights is, of course, paramount in our concerns," Hickey said. "I think that we would very much want to see that military assistance given by the United States does not increase the number of human rights violations."

The delegation, which arrived in San Salvador Wednesday, includes Chicago Cardinal Joseph L. Bernardin and two U.S. bishops in addition to Hickey and O'Connor. Hickey and Bernardin are considered relatively liberal on Central American issues, while O'Connor is regarded as more conservative on the topic.

The Salvadoran church arranged the U.S. visitors' itinerary, and San Salvador's Auxiliary Bishop Gregorio Rosa Chavez escorted them here. This morning they met briefly and privately with U.S. Ambassador Thomas R. Pickering.

Earlier they stopped in Nicaragua, and they plan to return to the United States Saturday.

Here they have had a busy program of meetings with bishops from El Salvador and other Central American countries and with a wide range of senior government officials and legislators. Yesterday they visited a refugee camp here in the capital and an orphanage outside it.

The delegation is to prepare a report on its visit for the administrative committee of the U.S. Catholic Conference. The U.S. church will use information gathered here in preparing testimony for Congress and in speaking at home on Central American issues, Hickey said.