The Reagan administration, while conceding that El Salvador's human rights record is "not perfect" nor "as great as desired," yesterday certified to Congress that the efforts of the government there to curb abuses and move toward democracy justify continued U.S. military assistance.

The certification, which had been expected, was forwarded to Congress by Secretary of State George P. Shultz, acting on behalf of President Reagan. In a tacit attempt to rebut charges by human rights groups that widespread abuses persist in El Salvador, the certification was accompanied by a detailed report setting forth the administration's reasons for its opinion.

Since January, 1982, Congress has required, as a condition for continued military aid, that the president certify every six months that Salvadoran authorities are making significant efforts to comply with internationally recognized standards of human rights, end widespread torture and murder of civilians by security forces, institute economic and political reforms and cooperate in bringing to justice the murderers of six Americans.

Yesterday's report, the third since the requirement was established, concluded: "El Salvador has made progress on all of the elements specified by Congress . The situation is not perfect, and the progress was not as great as desired, but it is progress nonetheless. The Government of National Unity is making serious efforts to improve the situation."

At a news conference, Thomas O. Enders, assistant secretary of state for inter-American affairs, acknowledged that at least "two important areas of weakness" remain in the Salvadoran record. He identified them as stemming from problems in the judiciary system that have thwarted bringing to justice some of those who the United States believes were responsible for killing two of the Americans, and that have seen the courts refuse to punish soldiers and security officers involved in rights abuses.

"This, we think, is a serious lapse," Enders acknowledged.

However, both he and Elliott Abrams, assistant secretary for human rights, contended that the overall record since 1980, when the United States began intensive support of the fight against leftist guerrillas seeking to win power in El Salvador, justifies continuation of the $25 million in military aid presently earmarked for that country.

Reagan, in a televised interview with high school students yesterday, made clear that he will not abandon his high-priority policy of helping to block the Salvadoran insurgency, which he described as an attempt to spread communist influence in the hemisphere.

Referring to criticism of the U.S. efforts, the president said, "The El Salvador situation has been distorted by a worldwide propaganda campaign, and I believe this stems from the Soviet Union by way of Cuba. It is a foothold they're attempting to establish here in the Western Hemisphere, on the mainland of North-South-Central America, of a communist state, similar to Cuba."

Despite the president's arguments, a number of private rights organizations that have been critical of U.S. policy toward Central America condemned the administration's action.

The Council on Hemispheric Affairs called it "certifying the uncertifiable"; the Americas Watch and the American Civil Liberties Union, in a joint statement, charged the administration with "playing a numbers game" that greatly understated the number of murders in El Salvador.

Enders, while not replying directly to such charges, said the death counts offered by other groups were larger because they include casualties from the fighting between guerrillas and government forces. The administration, he said, based its findings on recorded deaths of civilians, and he displayed charts showing a steady decline in the number of people killed in El Salvador since 1980.

Since Congress is in recess, there were no clear-cut indications of how the certification will be received on Capitol Hill. Sen. Christopher J. Dodd (D-Conn.), traveling in Latin America, issued a statement in Brazil contending that democratic leaders in the region regard the U.S. emphasis on fighting the guerrillas rather than attempting to foster negotiation as misguided.

"It is the wrong signal at the wrong time in the wrong place," Dodd said.

However, administration officials, while expecting some rumbles from Congress, are known to believe that congressional opposition on Central America policy has abated and that the president will not face any great danger in pressing for further military aid to El Salvador.

The administration had requested $60 million for such aid in this fiscal year, but Congress, which failed to pass a foreign aid bill, settled for a continuing resolution that kept security assistance at $25 million. Enders said that the administration has not yet decided whether to seek a supplemental appropriation.

In regard to the murder of American citizens, the report noted progress toward prosecuting five former National Guard members suspected of killing four woman missionaries, and said the evidence indicates that "the accused acted on their own and not pursuant to higher orders."