The radical leftist structure that helped channel arms to guerrillas in neighboring El Salvador and threatened to begin serious antigovernment action here has suffered a series of major setbacks in the last few months.

Suspected leaders have disappeared or been put under surveillance and seven "safe houses" containing contraband arms have been uncovered since Nov. 27.

A spokesman for the U.S. Southern Command in Panama said the supply network in Honduras appeared still to be in operation.

"When you shut down one area it will just spring up another place," he said. But, according to both Honduran military officers and leftist sources here, the original organization, at least, is close to destruction.

This is an apparent success for Washington, which repeatedly has portrayed interdiction of guerrilla arms shipments as a key to the Salvadoran conflict. The circumstances, however, cause many Hondurans to worry that short-term gains may lead to serious long-term consequences, drawing relatively peaceful Honduras ever deeper into the Central American quagmire.

Hondurans who watched closely as neighboring countries fell prey to violent leftist revolution and reaction from rightist paramilitary groups now see the beginnings of the same pattern here.

Of particular concern are the "disappearances" of political dissidents, which some Hondurans and diplomats believe are linked to the successful disruption of radical leftist organizations here.

Disappearances, or abductions of suspected subversives are commonplace in El Salvador, Guatemala and the military-ruled countries of South America where the authorities often deny any knowledge of the suspects' whereabouts, thereby evading responsibility for the subsequent interrogation, torture and murder of the suspects. Human rights groups generally believe these abductions are carried out by groups within the military or groups closely linked to the armed forces.

Until this year such disappearances were rare here. There have been more than 60 since February.

"That is worrisome and we've said so. It's not the quantity that preoccupies us, It's the system, knowing that it exists and is in motion," said Ramon Villeda, a prominent figure in the Honduran Liberal Party's left wing.

Villeda noted that the Sandinista revolution in Nicaragua gained tremendously from popular reaction against government repression there.

By contrast, he said, in Honduras, "When we've had military governments they haven't been bloody. There hasn't been official crime. They've gone along with the Labor Code, agrarian reform, a free press, and because of that the left has been given little sustenance." But in the cycle that leads to insurrection, said Villeda, "the first step is that people disappear."

A university professor cited three essential aspects of what he called "the new repressive policy in effect since the beginning of the year": It is preventive in character, designed to preclude the development of any strong radical organization; it is selective, aimed mainly at Salvadorans living in Honduras and Hondurans who might cooperate with them, and "most important, the repression is clandestine. The military denies having any political prisoners. They don't capture them, they kidnap them."

Several of the people who have disappeared are members of the communist Revolutionary Union of the People and militant student organizations that Honduran military officials, including chief of the Honduran Public Security Forces Col. Gustavo Alvarez, identify as the core of the subversive network here.

Among those who have disappeared recently, according to reports of their relatives and witnesses who saw them abducted, are Tomas Nativi, a leader of the Revolutionary Union of the People; Fidel Martinez, a former leader of the Honduran Communist Party, and Manfredo Velasquez of the Revolutionary University Force.

Others had no known political connection. One, Oscar A. Colindres Campos, was working for a government agency on a statistical survey related to a government corruption scandal, according to his sister, Ediltrudep.

The military consistently has denied any involvement in the disappearances, going so far as to bring legal action for "calumny" against some of the most vociferous relatives of the missing.

Maj. Julio Cesar Chavez of the Honduran National Department of Investigations suggested the disappearances are faked.

"Say person 'X' disappears. Sometimes they kidnap themselves. It has happened that a father searches for his son in all the police stations, doesn't find him and comes to think maybe the son is fighting with the Salvadoran Farabundo Marti Front. We're very clear about this. If we have someone, we say so."

But the Honduran government denied for more than a year that it was holding Salvadoran leftist leader Facundo Guardado, only to release him in March as part of the ransom for a hijacked airliner.

Asked about this case, Chavez said, "Well, yes, undoubtedly at the beginning we were denying we had him. Then we did some investigations. Well, everyone was aware that he had been detained."

Said one Liberal Party politician: "We think that the Army is responsible for some disappearances and not for others. But since the Army has lied it is assumed by the public that they do them all."

At a recent reception in the U.S. ambassador's residence, Col. Alvarez, one of the most powerful commanders in the country, outlined what he considers necessary tactics for eliminating subversive groups. While in no direct way acknowledging government involvement in the disappearances, Alvarez said members of subversive organizations have to be picked up and made to talk quickly before other members are aware of what has happened.

The left is organized in cells that are in regular contact, Alvarez said. If other cells do not receive an expected phone call before a given time they change location, go deeper into hiding.

This is the same analysis that dominates military thinking in Argentina, Chile and other countries where leftist movements have been crushed and thousands of people have disappeared. There are numerous reports that Chile, Argentina, Uruguay and Colombia are now providing technical help and advice to the Honduran military, but none of these reports could be confirmed.

Certainly most of the military assistance -- $10 million and about 20 advisers -- comes from the United States.

Some of the families of the missing see a link between U.S. policy and the fate of their relatives, with the Reagan administration's anticommunist rhetoric and emphasis on arms interdiction supplying an apparent justification for such actions.

They note that the only two persons who recently disappeared and then resurfaced, Socialist Marco Virgilio Carias and university professor Rogelio Martinez Reina, say they were repeatedly questioned about arms trafficking and Salvadoran contacts during the nine days they spent blindfolded, tortured and with little food and water in clandestine cells.

A senior U.S. official in the region denied any U.S. complicity in the disappearances.

"One of the things we talk to the host government about, obviously, is the interdiction of arms," said the official. "But there's a big gap between our encouraging them to stop it the arms flow and telling them the way to do it is haul people in off the street and 'disappear' them. It's implied that we want them to do it legally. . . . Well, more than implied.

"The U.S. advisers in Honduras are decent fellows who wouldn't knowingly lend themselves to this," the official added. "The problem is they may not make the connection as quickly as some of the families" of the missing persons.

Most analysts believe that Honduras, despite widespread poverty, is not yet in a condition to support violent revolution, and see the greatest danger to stability not in the limited actions of subversives here, but in the apparent response of the Army.

"For now," said a European political analyst who has studied regional problems for more than a decade, "Alvarez has been totally successful in eliminating the infrastructure supplying the Salvadoran guerrillas." He added that "there's no such thing as secrecy in this country, so at this point it's no big problem to eliminate the revolutionary left. The problem is that those people who survive are going to be serious people like those you have now in Guatemala."

The Nov. 29 election of a civilian president, the Liberal Party's Roberto Suazo Cordova, was seen as a rejection of both leftist and rightist extremism -- "a desperate cry of the people for moderation," as one former Cabinet minister put it.

But the new administration faces tremendous economic problems and may have to go along with whatever tactics the military wants to use against suspected subversives to avoid a confrontation with the Army that, given many precedents in Honduran history, could easily result in a coup.

"Honduras is slowly converting itself into a terrorist state," said a newpaper columnist, "and the new government's only choice is to legitimize this process with silence or confront the military and insist that all its actions, even if repressive, take place under the law. If the Liberal government doesn't feel supported by the United States in this process it will never try it."