President Reagan said in an interview published yesterday that six Soviet vessels are en route to Nicaragua "with more arms," and warned again that the administration would not tolerate shipment of MiG jets to that country.

White House spokesman Larry Speakes moved later to soften the Reagan remarks, saying "the man is assuming from appearances" of crates on board the six ships that they are carrying arms, but does not know for sure. "We make the assumption that there are arms on these ships," Speakes said, but "we're just not prepared" to say what kind.

A well-placed military source in Managua told Washington Post correspondent Robert McCartney on Tuesday that he was unaware of any Soviet arms shipments en route to Nicaragua at this time.

The Reagan-Speakes sequence was the second time this month the administration has suggested possible delivery of high-performance jets to the leftist Sandinista government of Nicaragua, then backed off.

The first report surfaced in leaks Nov. 6 as presidential election returns were being counted. It alarmed the world, because the administration has said repeatedly that such an event would change the area's power balance and would spark some undefined U.S. response, possibly a military one.

No MiGs appeared when the suspect vessel docked in Nicaragua, but the Sandinistas called a nationwide alert and prepared for a U.S. invasion.

A senior Nicaraguan Foreign Ministry official said of the new remarks yesterday: "We've already said it: there are no MiGs coming in the near future." But he also said "we are not going to stop having relations with the Soviet Union or any other nation, and we are not going to say what is coming on ships."

The official said that Reagan was evidently trying to "minimize the political impact" of Nicaragua's diplomatic victory Monday when the International Court of Justice in The Hague agreed to consider a Nicaraguan suit against the United States over U.S. military and paramilitary activities aimed at the Sandinista government.

"They are trying to convince public opinion that Nicaragua is a military warehouse," the official said.

In a White House transcript of the interview with The Washington Times, which was conducted Tuesday, Reagan said he is still not convinced that the first ship was not delivering jets.

"We can't prove that it was, we can't prove that it wasn't," he said. "But there are six more Russian ships, as nearly as we can count, that are on their way to Nicaragua now with more arms."

The president said jets would be "a threat to the area and to the hemisphere." He said the United States would not "raise Cain over a purely domestic type cargo . . . but we are in contact with the Soviet Union" on the question. He added that the ships had touched at ports where there were "crates that could contain" MiGs, and that one of those ports might have been in Libya.

If the vessels do contain high-performance jets, he said, "We have let the Soviet Union know that this is something we cannot sit back and just take."

State Department officials said yesterday they had no confirmation on the number, origins or whereabouts of the ships or their cargo.

Reagan assailed Congress as "shortsighted and, in fact, irresponsible" in cutting off U.S. aid to rebels who are fighting the Sandinista government, and said he would push to renew the aid in February.

A senior White House official defended that policy, saying the rebels had distracted the Sandinistas enough to reduce the help they had been giving to leftists in neighboring El Salvador. The Salvadoran government, he said, had been losing its war against leftist guerrillas but now is winning. He called overall U.S. policy in the area "reasonably successful."

In a speech to the National Press Club, Defense Secretary Caspar W. Weinberger condemned an "unprecedented" arms buildup in Nicaragua, saying 15,000 tons of weapons will have been delivered from Soviet-bloc countries by the end of 1984. Arms imports in 1981 were 790 tons, Weinberger said.

Meanwhile, Secretary of State George P. Shultz met with a high-level delegation from Honduras to discuss the Hondurans' proposals for a renegotiated treaty governing U.S. relations with the Central American country and for increased economic and military aid.

Headed by Honduran Minister of the Presidency Ubodoro Arriaga, the delegation included the Joint Chiefs of Staff chairman, Col. Efrain Gonzalez Munoz, and Finance Minister Manuel Fontecha. Foreign Minister Edgardo Paz Barnica was hospitalized and canceled plans to attend, Honduran diplomats said.

The Hondurans have made it clear they feel undercompensated for the militarization of their country that the United States has achieved since the Sandinistas took power in neighboring Nicaragua in 1979. While building eight bases, two radar stations and several ammunition depots, the United States is planning to provide only about two-fifths as much economic aid to Honduras as it is to El Salvador: $139 million compared with $341 million in fiscal 1985.

Honduras is also uneasy about El Salvador's growing military strength. The two nations fought a brief border war in 1969 and tensions remain high.

"We don't expect concrete results now, just an advancing of the process," said Moises Starkman, a Honduran presidential adviser. "There will also be talks in Honduras and we expect something concrete in a couple of months."