A leading figure in El Salvador's Roman Catholic Church today publicly backed U.S. Ambassador Deane R. Hinton in his appeal to the government and courts to crack down on rightist murder squads and their political backers.

The prelate, San Salvador acting Archbishop Arturo Rivera y Damas, also said that Hinton's estimate that 30,000 people have been murdered since the civil war began in 1979 "falls below the truth" rather than exaggerating the killing, as government leaders have insisted in strongly criticizing Hinton.

The outspoken comments by Rivera y Damas, in a sermon at mass today and remarks to reporters afterward, spotlighted the church's prominent political role in El Salvador. During the past decade, priests and prelates have become champions of the poor here, particularly in the struggle against human-rights abuses by sections of the Salvadoran security forces believed guided by rightist leaders.

The 8 a.m. Sunday mass in San Salvador's unfinished cathedral has become a semipolitical event. The archbishop's predecessor, Archbishop Oscar Arnulfo Romero, was assassinated March 24, 1980, after making the ceremony a forum for criticism of the government.

Rivera y Damas' sermon today marked the first public show of support here for Hinton's warning in an Oct. 29 speech here that Congress could force a halt to U.S. economic and military aid to El Salvador unless the country's human-rights record improves.

The speech, to the American Chamber of Commerce meeting, jolted the leadership here, amounting to a noisy and unwelcome departure from the "quiet diplomacy" espoused until now by the Reagan administration on human rights.

Several prominent groups -- including the Salvadoran Chamber of Commerce, the Salvadoran Industrial Association and the National Free Enterprise Association -- have denounced Hinton during the past week. They have accused him of intervening in internal Salvadoran affairs, acting like a Roman proconsul and wounding the country's honor and national sovereignty.

President Alvaro Magana and Defense Minister Jose Guillermo Garcia, while avoiding such strong language, suggested that Hinton's estimate of 30,000 political and criminal murders in addition to combat deaths was higher than the real toll, without offering their own estimate.

Rivera y Damas, whose church offices have sheltered human-rights organizations keeping a tally of the killing since the violence began, supported Hinton's estimate. "As far as he is concerned, it is possible that many errors accompany the declarations, or rather the denunciations, made by Ambassador Hinton about our judicial power," the archbishop said in his sermon.

"But it seems that no serious entity in our country fails to recognize the substance of what he said. Besides, the church, which has always condemned foreign intervention of any kind, judges that to be credible, the accusations that are being made against Hinton's recent statements must also include condemnation of the United States in economic and military affairs."

This was a reference to U.S. economic and military aid here, which amounts to about $230 million this year, including 50 military advisers working with the Salvadoran Army against leftist guerrillas.

The U.S. help is considered crucial to the government's ability to continue the war. For the U.S. aid to continue, however, the administration must certify to Congress every six months that the Salvadoran government is making progress in curbing human-rights abuses. The next certification is due in January.

"The majority of the people would agree with it," the archbishop said of Hinton's call for reform of the judicial system to deal with the abuses.

The church leader also mentioned the recent arrests of leftist and labor leaders that the government alleges had ties to the insurgent political apparatus, the Democratic Revolutionary Front. He expressed satisfaction that their names have been announced by the government -- an indication that they probably had not been murdered -- but sharply criticized their secretive arrests by heavily armed gunmen in civilian clothes.

"We ask, if there is a good reason to hold these men, why do the authorities take off their uniforms to pick them up?" he said. "These detestable practices, which the church condemns in the name of humanity . . . would be alleviated if the judicial power of our country acted as it should."