The Reagan administration, armed with new and clear-cut evidence that police in El Salvador have inflicted torture on Salvadoran civilians in recent months, has warned top governmental authorities there that this practice is likely to have major repercussions in the United States.

Despite the evidence that prompted the U.S. concern and intervention, the administration is planning to certify to Congress Wednesday that El Salvador "is making a concerted and significant effort to comply with internationally recognized human rights" and "is achieving substantial control over all elements of its own armed forces, so as to bring to an end the indiscriminate torture and murder of Salvadoran civilians by these forces."

Under a requirement imposed by Congress last year, the administration must make these certifications every six months in order to continue to supply U.S. military aid to El Salvador.

Official assurances to Congress on these points were supplied by the administration in January, but critics have charged that the statements were a sham.

According to information available here, a particularly gripping account of torture by the National Police in May came to the attention of the U.S. Embassy and generated a stir when reported to Washington.

The case reportedly led to a special plea from U.S. Ambassador Deane Hinton to Salvadoran President Alvaro Magana late last month to put a stop to the practice before severe damage is done to U.S. public support.

The case in point involved a Salvadoran volunteer for the Green Cross, a leading humanitarian agency. The volunteer was arrested on suspicion of providing supplies to guerrillas. In fact, according to the volunteer, he had distributed medicines received through international channels to displaced persons in an open and above-board fashion.

The torture is reported to have taken place over several days in a secret part of the National Police headquarters in downtown San Salvador, in a suite of soundproof rooms inaccessible to the International Red Cross and other groups that visit prisoners.

In one torture session, the victim was strapped to a rotating wheel, similar in function to the medieval rack, causing great muscle strain and pain. In another torture, he was beaten severely and forced to inhale lime.

In a third operation, which the torturers called "the Carter," in an ironic reference to former president Jimmy Carter, a champion of human rights, the victim was strung up by ropes tied to his hands and feet while severe pressure was applied to his testicles by means of a wire.

The State Department was informed that the victim was in great pain and psychological distress when seen by an American official after his release from custody. The official had known the victim before and considered him reliable and credible.

According to official sources, the U.S. Embassy in San Salvador is in possession of several other documented cases of torture involving various government security forces.

But this one case apparently touched a raw nerve more than others because of its detail and credibility, and because of the requirement for the administration to report to Congress by Wednesday on the Salvadoran government's human rights performance.

As part of the drive to support a positive certification for El Salvador, the administration sent Elliott Abrams, assistant secretary of state for human rights and humanitarian affairs, on an unannounced inspection trip to that country.

Abrams said in a Cable News Network interview yesterday that he has recommended certification of El Salvador for continued military assistance.

In a telephone interview last week, Abrams said that he is familiar with the case that caused the recent governmental stir, but that he believes it should be viewed in the context of "a steady improvement in human rights performance, especially on the part of the National Police."

According to Abrams, the National Police commander, Col. Lopez Nuila, has "a strong commitment to human rights" that is not matched by some of the heads of other security agencies.

"I can't say they won't have incidents. But when you have a long, horrifying tradition of abuse of prisoners, it is significant when you start taking action to eliminate it," Abrams said.

A report made public last Tuesday by the American Civil Liberties Union and the Americas Watch Committee took a less optimistic view. Among the conclusions of the 272-page study:

"The government of El Salvador, during the period September, 1981, through July 7, 1982, has not exerted substantial control over the repressive actions of its armed forces. Indiscriminate torture and murder of Salvadoran citizens has continued during this period, and all branches of the security forces have been implicated in this repression."

The report charged that the Salvadoran government is engaged in a campaign of "systematic political murder" that disqualifies it from receiving U.S. aid, and cited an estimate from the legal aid office of the Archdiocese of San Salvador that government security forces committed at least 2,829 political murders in the first half of this year.

Another conclusion of the civil rights groups was that during the tenure of president Jose Napoleon Duarte the civilian part of the government did not exercise control over human rights violations by security forces.

"In the current Magana government, real influence over the armed forces still resides with those military authorities that held power in the previous government," the report said.

This conclusion would seem to be borne out by the cautious reaction of Magana to the plea by the U.S. ambassador for strong action to bring an end to torture.

The Salvadoran president reportedly was sympathetic with Hinton's viewpoint and suggestions, but also said it is a difficult and complicated matter to control abuses by security forces.