Ever since 1980, when he was among the first Nicaraguans to join the anti-Sandinista resistance, Jose Efren Martinez Mondragon had appeared to follow the typical career of the dedicated contra, or counterrevolutionary, guerrilla leader.

Formerly a sergeant in the National Guard of deposed dictator Anastasio Somoza, Martinez Mondragon worked his way up in the resistance movement from commander of a guerrilla training unit in Honduras to become a task force commander who regularly led missions inside Nicaragua. Just six months ago, he was commanding 180 contras on a patrol in Esteli province, deep inside territory normally controlled by the Sandinistas.

Today, however, Martinez Mondragon did something that no contra commander ever had done before: he flew home to Managua to be welcomed by his former foes as a defector. He will take advantage of a Nicaraguan amnesty law approved earlier this year that provides for a pardon for rebels who lay down their arms. Eight weeks ago, Martinez Mondragon and nine other persons, including two other guerrillas, sought political asylum in the Mexican Embassy in Tegucigalpa, Honduras. Initially the Honduran government refused to let him leave the country, although the others were permitted to depart for Nicaragua almost immediately, and his fate was uncertain until a week ago when the Honduran authorities finally let him fly to Mexico City.

The defection ended what Martinez Mondragon described as a prolonged personal ordeal of several years as he grappled with his own doubts about the guerrillas' cause and, even more, about their behavior in the field. In a four-hour interview here last night, he said he left the contras in disgust with what he said were their routine practices of murder, kidnaping and rape of Nicaraguan civilians.

"They are kidnaping and killing people who just want to work," the 26-year-old defector said. "This wasn't a struggle. It was banditry."

While there have been news reports of individual incidents of alleged killings and abductions by the contras of Nicaraguan civilians who were, or were believed to be, Sandinista sympathizers, Reagan administration officials in the past have denied the validity of claims that such practices were routine and characterized the claims as propaganda.

In another assertion that was likely to be controversial, Martinez Mondragon said that the Honduran, Salvadoran and Guatemalan armies have supplied the contras with the bulk of their ammunition and other military supplies since the CIA stopped funding them a year ago.

Spokesmen in Miami and Honduras for the rebel group Martinez Mondragon belonged to were unavailable today for comment on his specific allegations.

Because of the severity of his charges and the unprecedented nature of his defection, Martinez Mondragon's change of heart could contribute to the political debate that extends from Managua to the U.S. Congress. The guerrillas previously have drawn criticism for human rights abuses from some unofficial U.S. monitoring groups. This has become a factor in the U.S. debate over whether Washington should resume financial backing for them.

Several former Sandinista leaders, such as Arturo Cruz and Eden Pastora, and many sympathizers of the Sandinistas have broken with Managua's government and are allied with the rebels. Martinez Mondragon, a middle-level contra field commander, is the first to go the other way.

The defection already has triggered a flurry of activity by several of the players involved, either to control the damage or maximize it.

The Nicaraguan Democratic Force, the largest of the rebel groups and the one to which Martinez Mondragon belonged, already has suggested that the defector had lost some of his mental faculties because of a motor vehicle accident. The force, known by its Spanish initials FDN, also has charged that Martinez Mondragon's lover was a Sandinista spy who may have encouraged the defection.

For its part, the Nicaraguan government wasted no time making the defector available to the media, presenting him both at the interview last night and at a news conference upon his arrival in Managua this morning.

In the interview, Martinez Mondragon alleged that the contras have regularly killed Nicaraguans who refused to join the rebel cause after crossing the border into Honduras or after being abducted and brought there by the guerrillas. He said that there were several clandestine cemeteries for such victims along the Nicaraguan-Honduran border, including one near a hamlet called San Judas in Honduras' Choluteca province, and another at La Lodoza in El Paraiso province.

"If you won't fight, then they think you are a Sandinista infiltrator and kill you," he said.

He said the armed forces of Honduras, El Salvador and Guatemala currently are providing the FDN with the bulk of its ammunition, uniforms and boots. He said he had seen Honduran military trucks and helicopters deliver ammunition and other supplies to contra camps, and that he had learned from friends who handled the rebels' supplies that these three countries' armies were the principal source of materiel.

The FDN's base camps are inside Honduras just across the border from Nicaragua, and the defector said that Honduran Army officers control all deliveries of military supplies to the contras.

Since Congress stopped the CIA from funding the guerrillas a year ago, the source of the rebels' military supplies has been something of a mystery. The rebels say they have continued their fight with the aid of private donations, but several reports have surfaced that the Honduran, Salvadoran and Guatemalan governments were playing an important role.

Martinez Mondragon said that other contra commanders had told him that "the CIA advisers arranged for the Salvadoran, Guatemalan and Honduran armies to provide materiel" to the FDN. He did not say when the CIA supposedly had done this, however.

He said guerrillas frequently had raped civilian women in Nicaragua and abducted them for sexual use.

During a patrol in Nicaragua's Jinotega province last August, the defector said, he came across a group of 40 families near Wina who said that they had been abducted by another patrol from the San Jacinto regional command. This patrol had abducted and raped eight young women from the group, and had killed eight young men who refused to join the rebels, he said.

At that time, Martinez Mondragon said, he radioed FDN military leader Enrique Bermudez to complain about the treatment of the civilians. Bermudez told him "to stop interfering in business that doesn't affect you," the defector said. This was only one of several times that Martinez Mondragon complained to FDN leaders about abuses by the rebels and received unsatisfactory responses, he said.

The interview was conducted in a sitting room at the Nicaraguan ambassador's residence in Mexico City, but the defector said that he had not been pressured to grant the interview and had not been briefed beforehand by Sandinista officials. Nicaraguan Embassy officers wandered through the room from time to time during the talk, but their presence did not seem to affect Martinez Mondragon.

The defector acknowledged that he was seriously hurt in the vehicle accident, when he struck his head hard and was unconscious for a week. He spoke slowly, occasionally lost his train of thought and said that his head still hurt "deep inside" from time to time.

While the FDN has suggested that he cannot be trusted because of brain damage, the FDN did entrust him to command several missions inside Nicaragua after the accident had taken place.

Martinez Mondragon expressed fears that the FDN would take reprisals against his friends or family. He said he believed the FDN's leadership was responsible for the deaths of his brother and two of his cousins.