The State Department, trying to explain away impressions left by President Reagan's Latin American trip, said yesterday that the president had not meant to say he was "surprised" to discover that Latin nations are "individual countries."

Nor had he meant to say that he has decided to certify human rights progress in El Salvador to permit continuation of U.S. aid there, and he has not decided to permit sale of spare helicopter parts to Guatemala, either, a senior State Department official said.

The department seemed especially anxious to forestall any explosions of wounded Latin pride at the "individual countries" remark made by Reagan as his plane returned to Andrews Air Force Base late Saturday night. U.S. diplomats were fearful that his comments would be interpreted as a naive and tactless admission that all Latin Americans had seemed alike to him.

"I assume you want to get this thing as it was and is," the senior official told reporters at a background briefing. The official, who cannot be identified under the briefing rules, first implied that much reporting on the trip last week had been incorrect; when reporters then challenged him by quoting Reagan's words, he said the intent of the president's remarks had been misunderstood.

On Saturday, as Reagan was flying home from the five-day trip to Brazil, Colombia, Costa Rica and Honduras, he told reporters on Air Force One: "Well, I learned a lot . . . . I went down to find out from them and [learn] their views. You'd be surprised. They're all individual countries."

"Some subsequent press reports quoted the president as saying he was 'surprised,' " the senior official said yesterday. "That was not the case."

Instead, the official continued, Reagan, through his use of the term "You'd be surprised," had intended to suggest that many Americans, including perhaps those reporters on the plane, were probably not aware of the great differences among Latin countries.

Reagan, the official asserted, always has been keenly interested in Latin America, as evidenced by his meeting with Mexican President Jose Lopez Portillo shortly after Reagan was elected president. In fact, the official said, the purpose of last week's trip was "to mark the priority attention he wants to give to the hemisphere."

The other Reagan remarks about which the official was anxious to elaborate involved El Salvador and Guatemala. In both cases the administration's desire to defeat leftist guerrilla insurgencies has run into opposition from congressional critics who argue that the human rights records of the Salvadoran and Guatemalan governments do not justify U.S. military aid.

As a condition of continued security aid to El Salvador, Congress has passed legislation requiring the president to certify every six months that that country, among other things, is making progress in correcting human rights abuses. The next certification is due in January.

Last Friday, following a meeting in Costa Rica with Salvadoran President Alvaro Magana, Reagan was asked by reporters whether he would make such a certification to Congress next month. He replied: "On the basis of everything we know now, yes, of course."

That led to several press reports that the president had decided to make the certification. However, the senior official said yesterday that Reagan had not intended to give that impression and added that a final decision on the delicate issue is still to be made. The same official, who accompanied Reagan on the trip, noted that he had made that point in a press briefing immediately after the Reagan-Magana meeting, but that his remarks had been ignored in many press dispatches.

The Washington Post, in a dispatch from Costa Rica by correspondent Christopher Dickey published on Saturday, quoted the official as saying: "The questions involved in certification were discussed in detail [by Reagan and Magana]. However, no decision was reached on them . . . . This was not a certification exercise per se."

On Saturday, Reagan met in Honduras with Gen. Efrain Rios Montt, who seized power in Guatemala after a military coup earlier this year. Afterward, Reagan praised Rios Montt as "a man of great personal integrity" and said the Guatemalan had been getting "a bum rap" from critics of his human rights record.

That led to some reports that the administration, as had been widely rumored before Reagan's trip, intends to permit Guatemala to buy U.S.-made spare parts for helicopters used in its anti-guerrilla campaign. However, Post staff reporter Lou Cannon, in a report from Honduras published on Sunday, quoted an administration official as saying that no decision is likely on this aid request before January.

The senior official said yesterday, in reference to the helicopter parts, "That issue remains undecided. I can't say when it will be decided."

He also insisted that the question of resuming military aid to Guatemala, which has been suspended since 1977, is not now under discussion and noted that the helicopter parts fall within the category of commercial sales. While that is technically correct, Guatemala wants the equipment for military purposes; and the official acknowledged that the administration has a commitment to consult carefully with Congress before authorizing such sales.

Asked whether he agreed with Reagan's assessment of Rios Montt, the official said the Guatemalan appeared to be trying to clean up rights abuses and corruption and, conceding that the regime's record is mixed, said: "I think it adds up to a bum rap. It's the old question of the better being the enemy of the good."