A right-wing death squad that publicly has targeted President Jose Napoleon Duarte and his supporters killed three youths last week, including the 14-year-old son of a pro-Duarte peasant union leader, the father of one of the slain youths said today.

The killing, which prompted the U.S. Embassy to issue a communique expressing its "outrage," was discovered early Saturday morning by the union official, Alirio Montes. Although the embassy statement mentioned only the Montes youth, Montes said the bodies of two unidentified youths had been found with him.

In an interview, Montes said he discovered the deaths after he received a telephone call early Saturday morning from a group called the Secret Anticommunist Army. The caller told him where he could find the body of his son, Boris.

The bodies of the three youths were found by the side of the road near the capital's Mariona prison, an area long used by the death squads for dumping the bodies of their victims, Montes said. All three youths had been shot at close range and each had the death squad's Spanish initials "ESA" carved on his forehead, he said.

Tonight, a U.S. source said that a search of morgues for the body of the Montes youth had proved negative. Despite their strong condemnation of the apparent killing, U.S. officials here cautioned tonight that the initial reports of the slaying may not have been as stated. But the embassy did not retract yesterday's statement.

Montes could not be reached for further comment.

The reported killing provoked one of the strongest statements yet on death squad activity from the U.S. Embassy, which had applauded a decrease in the number of such killings following Duarte's election in May. The communique, issued last night, said, "there are no words to properly express our outrage that once again murderous thugs masquerading as paramilitary 'patriots' have taken innocent life, this time that of a 14-year-old boy."

The communique urged the Duarte government to "move quickly and forcefully to bring about a full, vigorous investigation of this sickening deed" and to bring the "full force of law to bear" on the culprits.

Alirio Montes, who said he had been the target of repeated death squad threats because of his work for the Salvadoran Communal Union, said today that a note had been pinned to his son's chest warning the father to quit working for the peasant union.

The murders were the first to be claimed by the Secret Anticommunist Army since it issued a communique Oct. 13 accusing Duarte and his suporters of "high treason" because of Duarte's scheduled meeting two days later with leftist rebel leaders. The communique called Duarte and his supporters "enemies of the fatherland" and said they would henceforth "be targets of our military actions." The Secret Anticommunist Army is one of the main rightist terrorist groups active here.

Whether Boris Montes and the two others had been selected for death because their families were supporters of Duarte was not immediately clear.

Alirio Montes, the publicity director for El Salvador's largest union, said threats made against him in recent months have focused on the fact that he ran a radio program for peasants that often had been critical of the extreme right.

"They wanted to stop my radio program because it sought to educate the peasants about their rights," Montes said today at his union headquarters in the town of Santa Tecla outside the capital. "You know, in our country just to educate the peasants is a sin."

The killing of his son, a student, came on the eve of ceremonies by the union to celebrate its 13th anniversary. It was exactly a year before, on the eve of the union's 12th anniversary, that rightist leader Roberto D'Aubuisson went on television to denounce Samuel Maldonado, then union president, as a communist and to accuse the AFL-CIO-supported union of funneling money to leftist guerrillas.

Since Duarte took office in June, Maldonado has been head of the Salvadoran Institute of Agrarian Transformation, the government agency in charge of El Salvador's land reform program.

Montes, who is separated from his wife, said today that he had been at his own home working on a speech for the anniversary celebrations when Boris was kidnaped from his mother's house early Saturday morning. The speech, he said, was about Rodolfo Viera, the peasant union leader who also served as head of the land reform institute until he was assassinated here along with two AFL-CIO officials on Jan. 3, l981.

Three days before his death, union officials said, Boris and a friend had been picked up in the streets of the city by armed men in civilian clothes.