President Reagan said tonight that "on the basis of what we know now," he would certify human rights advances in El Salvador that are the key to continued U.S. aid to that nation.

But in a briefing after Reagan's remark, an administration official tried to play down the president's words, emphasizing that no decision on certification had been made.

Reagan's statement came after a one-hour discussion with Salvadoran President Alvaro Magana immediately following Reagan's arrival here, the third stop of his four-nation Latin American tour.

Reagan arrived from Bogota, Colombia, where he received a stern reception and was urged to shift U.S. policies in Latin America. Details on Page A20.

As the president was leaving the Cariari Hotel, where he met Magana, Reagan was asked whether he was satisfied with El Salvador's progress on human rights. "They are trying very hard and making great progress against great odds," Reagan said.

The president was then asked whether he would certify U.S. aid for El Salvador in January. "On the basis of everything we know now, yes, of course," he replied.

A senior American official briefing reporters later pointed out that the issue of certification is a very complex one. In what appeared as a softening of Reagan's remark, he said, "The questions involved in certification were discussed in detail. However, no decision was reached on them . . . . This was not a certification exercise per se."

As recently as Oct. 29, U.S. Ambassador to El Salvador Deane R. Hinton made a speech before Salvadoran businessmen that strongly suggested the administration "would be forced" to cut off aid because of continuing problems with human rights--in particular with the prosecution of Salvadoran military officers implicated in the killings of four American churchwomen and two U.S. land reform advisers.

Reagan's remark came only one day after a Salvadoran court dismissed all charges against Lt. Rodolfo Lopez Sibrian. His release in October, after evidence was presented implicating him as having ordered the killings, prompted Hinton's speech.

U.S. aid to El Salvador amounts to $250 million in economic support and $81 million in military assistance in fiscal 1982. Hinton said in an interview late last month, "I don't really think they'd have much chance of success without our assistance."

The U.S. executive branch must certify to Congress every 180 days that progress has been made in the areas of land reform, the democratic electoral process, control of human rights abuses and progress in prosecuting the murderers of the U.S citizens. Those cases include the killing of four Catholic Church women Dec. 2, 1980, and the two agrarian advisers affiliated with the AFL-CIO in January 1981.

The senior U.S. official cited as areas of improvement the fact that the two gunmen in the agrarian case had been ordered to trial, as have five Salvadoran national guardsmen accused of killing the churchwomen.

A spokeswoman representing relatives and friends of the four slain women, two of whom were Maryknoll nuns, charged in Washington Wednesday that trial proceedings were designed to cut off any further investigation into the possible involvement in the murders of high Salvadoran military or political figures.

"We believe that the trial as it is designed to be carried out cannot lead to justice," Sister Helene O'Sullivan, director of the Maryknoll Order's Office of Social Concerns, told a press conference.

Reagan's arrival here in the most tranquil of Central U.S. capitals for meetings with Magana and Costa Rican President Luis Alberto Monge was the most upbeat of his trip so far, according to officials in his entourage.

Scores of school children were on hand, waving American and Costa Rican flags as Air Force One touched down shortly after dusk. Reagan and Monge greated each other with effusive embraces.

Twenty years ago, president John F. Kennedy came here boosting a program to stop the spread of communism in a politically explosive environment by providing U.S. economic and military aid to developing democracies.

Tonight Reagan arrived with the same announced goal. He is to travel Saturday to Honduras, the last stop of his tour, for talks with the Honduran and Guatemalan presidents.

Where two decades ago the spark of concern and the center of attention was the Communist island of Cuba, today that focus is on revolutionary Nicaragua, but the worries and responses are similar.

With fragile and floundering economies, deep-rooted social divisions and often authoritarian rule, Central America has seethed for much of its modern history.

When crises erupt, as they have in Nicaragua, El Salvador and Guatemala during the last four years, Washington attempts to help redress these problems. A parallel policy is to neutralize any force that would try to take advantage of them.

Reagan's visit, intentionally short on substance and long on symbolism, is intended to emphasize positive assistance for the neighbors of Nicaragua. Before his arrival, efforts were made to downplay and at least temporarily defuse the overt and covert pressures being put on the Sandinista rule in Nicaragua.

Eden Pastora and other well-known anti-Sandinista rebels based in San Jose have quietly left the capital, and perhaps the country, for a few days, according to some of their associates. Joint U.S.-Honduran military maneuvers scheduled for this week were postponed indefinitely. Camps in Honduras that have served as bases for Nicaraguan counterrevolutionaries have been dispersed.

But Reagan's visit is nevertheless seen as part of an ongoing effort to isolate and pressure what some U.S. diplomats call "the deliquent country." Senior U.S. officials have said repeatedly that the Sandinistas represent an "unacceptable threat" to the region's security and, because of their close ties to Moscow and Havana, are a threat to the United States.