Washington — A new human rights report points to the formidable difficulties which El Salvador's President-elect will face in attempting to curb death squads. President-elect Jose Napoleon Duarte meets today with American congressional leaders in an attempt to secure more aid for his government. Promising to deal with political violence, Mr. Duarte met with President Reagan here on Monday.
Assassinations carried out by the so-called death squads are a major issue with congressional leaders. But a report issued on Monday by Amnesty International, the London-based human rights organization, says that until now, at least, the Salvadorean government authorities have lacked the political will needed to investigate many thousands of unresolved violent deaths.
In the Congress, House and Senate conferees disagreed last week over a $62 million emergency military aid proposal for El Salvador. Senators favored the aid, but House conferees refused to approve it. The next stage in the legislative process will include House floor votes on this and other aid issues.
President-elect Duarte meets today with Congressman Clarence D. Long, the Maryland Democrat who chairs the key foreign operations subcommittee of the House Appropriations committee. Mr. Long's word on Central American issues carries great weight with other congressmen.
Long has spoken favorably of Duarte in the past, but, as an aide explained it , the congressman is uncertain as to whether Duarte will have the power to do the things he has pledged.
A few years ago, when Duarte served as president and as a member of a civilian-military junta, Long had the impression that the military held the greatest power and that Duarte's powers were limited.
''We will see where Duarte stands on human rights and death squads, on negotiations, and on improvements in the military,'' said Long's aide. ''We will try to feel out what his relationship with the military is.''
Congressman Long is persuaded that if the Congress approves all of the aid which is requested, no matter what the circumstances, the Salvadorean military will never be reformed.
The administration is arguing, however, that additional aid to El Salvador will enhance the influence of President-elect Duarte.
Standing in front of the White House on Monday following his meeting with President Reagan, Duarte was asked by reporters to comment on the new Amnesty International report on El Salvador.
The 48-page report concludes that a ''large proportion'' of the killings of noncombatant civilians in El Salvador occurring since 1979 were executions carried out by the Salvadorean government's military and security forces and by civil defense personnel acting under the government's military command.
Duarte replied that he had been out of the government for two years and that it was time to look forward and not to the past.
In an appearance Sunday on the NBC television program ''Meet the Press,'' Duarte repeated a pledge that he has made to appoint a commission to investigate death-squad crimes.
The US State Department commented Monday on the Amnesty International report, arguing that it had been compiled nearly a year ago. A State Department spokesman said that El Salvador had made ''real progress'' against political violence and that death-squad killings had dropped sharply.
One test of the Salvadorean government's resolve is expected to come shortly in the trial of five former National Guardsmen accused of killing three American nuns and a lay churchwoman in December 1980. A Salvadorean judge last week set Wednesday as the trial date and selected a jury by lottery for the long-delayed case.
Public concern over this case led Congress to pass legislation requiring that progress be made in the investigation of the women's deaths as a condition for further US military aid to El Salvador.
According to the Amnesty International report issued Monday, it has largely been only in such cases involving political pressure from abroad that the Salvadorean authorities have initiated even the most cursory inquiries into the circumstances of violent deaths.
Even then, the AI report said, an investigative team sent to El Salvador by the US government shortly after the killings of the churchwomen was not allowed to interview potential murder witnesses or the local justice of the peace.
The AI report was prepared in large part on the basis of a trip to El Salvador conducted last year by a Spanish jurist, a US forensic pathologist, and an AI research expert.
In a speech delivered on May 9, President Reagan declared that the right-wing perpetrators of violence in El Salvador were not part of the government there. But the AI report, many news reports, and the State Department's annual report on human rights published earlier this year all suggest that some right-wing death squads have links with elements of Salvadorean government security forces.
The AI report contends that statements by defectors and highly placed politicians as well as by military and security officials have provided direct evidence for the conclusion that ''all branches of the Salvadorean security and military apparatus'' have been responsible for the large-scale executions of noncombatant civilians.
The report also points to circumstantial evidence such as the presence of units of the regular uniformed police or military forces in areas where arrests are made; plainclothes agents seen making arrests while accompanied by or observed by uniformed personnel; and assailants traveling in police or military vehicles and moving freely on city streets during curfew hours, unmolested at police roadblocks.