Vice President Bush has become the second high administration official in two days to express concern over the support that Catholic clergymen are giving Marxist revolution in places like El Salvador.

Bush, on the eve of Pope John Paul II's visit to Central America, on Tuesday told a private forum of prominent former officials and opinion leaders from North and South America that he is unable to understand how priests can reconcile their faith with Marxist ideas and tactics.

His remarks prompted Notre Dame's president, the Rev. Theodore M. Hesburgh, a member of the group, to reply that the endemic poverty and social injustice of the region can easily lead priests to make common cause with Marxists or anyone else seeking to change the established order.

Sources who were present said that, despite Hesburgh's explanation, Bush persisted in asserting his puzzlement at the attitudes of influential forces in the Catholic church toward Central America. Some quoted him as saying, "Maybe it makes me a right-wing extremist, but I'm puzzled. I just don't understand it."

These sources said the exchange between Bush and Hesburgh, while conducted with civility, created a considerable stir, particularly among the Latin Americans present. They said several participants speculated afterward that the administration may be trying to discredit the influence of the church in the area.

The administration in recent days has reiterated its determination to pursue a military solution to the Salvadoran civil war and has rejected anew the alternative, advocated by many churchmen, of trying to negotiate a political settlement with the insurgents.

Bush's remarks came a day after Secretary of State George P. Shultz, testifying Monday before a Senate subcommittee, went on the attack against "churchmen who want to see Soviet influence in El Salvador improved . . . . When you follow policies bound to result in that effect, that's what you're doing." Shultz also said, "There is nothing great about the way religion is treated in the Soviet Union." The Bush-Hesburgh exchange occurred Tuesday night during a closed meeting of the Inter-American Dialogue, which was formed last fall to address problems in U.S.-Latin American relations. Its chairmen are Galo Plaza Lasso, former president of Ecuador, and Sol M. Linowitz, whose various diplomatic assignments have included the negotiation of the Panama Canal treaties.

Several of the U.S. participants said they did not believe Bush was trying to pick a fight with the Catholic church, and added that they had sought to reassure their Latin American colleagues on that score.

But some also said that the Latins, who represented a broad spectrum of opinion, came away from the meeting with what one source called "a very bad impression of the Reagan administration's policies and a feeling that Washington is interested in dealing with the guerrillas only at gunpoint."

In response to questions from The Washington Post, Bush's office sought yesterday to minimize the situation and sound a conciliatory tone. A statement issued on behalf of the vice president said he had viewed the session as "an open and candid discussion and had posed an honest question of puzzlement to a lot of Americans."

The statement also quoted Bush as saying, "The answer from Father Hesburgh, one of my favorite people, to the questions about Marxism and the clergy was eloquent and useful to me. I'd be amazed if anyone could view the dialogue as anything but beneficial."

A spokesman for Bush added that the vice president had been speaking "in a joking manner to emphasize a point" when he referred to himself as "a right-wing extremist."

Since the session was off the record, neither Hesburgh nor the other participants would comment publicly on what happened. However, several, speaking on the condition that they not be identified, gave the following account.

Bush, putting aside a lengthy prepared statement, said he wanted "to hear and learn." During the ensuing discussion, Bush defended the administration's contention that it is imperative to be vigilant against the Marxist threat in Central America and then posed his question about the priests.

At Linowitz' suggestion, Hesburgh, one of two priests present, replied. He said it is true that Marxism and Catholicism are irreconcilable on a number of fundamental points, including the fact that "we Catholics believe in God, and they don't."

But he then went on to say that if one were to think of priests, with their mission of helping the poor, having to contend with starving children and oppressed peasants and slum dwellers "working all their lives for a few cents a day," it is not difficult to understand how they can "work shoulder-to-shoulder" with Marxists or others who seek to change the system in ways that will better the lives of these people.