SAN ONOFRE, Colombia :  In one of the most horrific chapters of Colombia's long civil conflict, investigators are unearthing scores of bodies from secret graves dotting this humid cattle-grazing region near the Caribbean, the victims of right-wing paramilitary groups now benefiting from generous concessions for pledging to disarm.

With dozens of people coming forward in recent months to complain of missing relatives, government and military officials now estimate that hundreds of farmers may have been killed and secretly buried in a terror campaign that began in the late 1990s.

The paramilitary groups, they say, kidnapped and killed their victims to seize land and in some cases weed out supporters of the Marxist guerrillas who have been fighting the government since the 1960s.

For years, fear kept the crimes hidden. But with the arrival this year of a new military commander who has secured the region, families finally began speaking out, despite lingering dangers that cost the life of one whistle-blower earlier this year.

So far, 72 bodies have been recovered from El Palmar, a vast farm outside San Onofre that was used as a local base by the paramilitary forces, whose militias control several coastal states.

From the dark, moist earth, the authorities have also uncovered bodies in several other villages and are working to locate graves in five other states, said Elba Beatriz Silva, coordinator of the attorney general's human rights office, which is overseeing a gradual process of exhumations that may expand even further.

"A lot of people here have disappeared - sons, fathers, mothers, brothers," said Ivan Wilches, 22, whose brother disappeared. "Every day there were people killed. They would pull them out of houses, breaking down doors. They would all wind up dead."

The discoveries have highlighted a brutal but overlooked component of Colombia's war - the disappearances of more than 3,500 people in recent years - and raised fresh questions about whether there will ever be justice for the killings.

The authorities say they have arrested 11 paramilitary fighters from the area, who face criminal charges. But the two suspected masterminds, according to local people and government authorities, are benefiting from a new Justice and Peace Law that offers them leniency in exchange for disarming.

The two commanders - Edward Cobos and his lieutenant, Rodrigo Mercado Pelufo, who ran the local 600-member militia - are ensconced in a government-run safe haven for 50 paramilitary commanders and could serve sentences as short as two years.

They and other militia members are not obliged to provide details of their crimes. If the authorities do press charges, the law gives them only 60 days to build cases, something human rights groups say will be nearly impossible.

The government, which has tried and failed for years to negotiate an end to the conflict with the guerrillas, says the law is needed to demobilize about 15,000 paramilitary fighters throughout the country who have taken up arms in recent years, adding to the violence.

The law has ignited fierce objections from those who fear that it will lead to a whitewash of some of the worst atrocities of a 41-year civil conflict in which 200,000 people have died.

But little attention has been paid to what is known as the "disappearing" of people, something more commonly associated with other Latin American conflicts, from El Salvador to Brazil to Argentina.

Since the 1990s, the tactic has been used with increasing frequency in Colombia. The Colombian Commission of Jurists says that 3,588 people vanished in this country from 1996 to 2004.

Many killings here are attributed to a paramilitary unit calling itself the Heroes of the Maria Mountains, which Cobos and Mercado Pelufo ran. The attorney general's office says that the group was engaged mostly in drug trafficking and corrupting local officials and that the killings helped it seize farmers' land and control cocaine-trafficking corridors to the Caribbean.

Officials say the paramilitary groups also killed those they accused of aiding the rebels, the few who dared complain, small-time criminals and even their own fighters who fell out of favor.

"Everyone knew about this, but no one said anything, because if you did they'd come at 3 or 4 in the morning and take you away," said Lorenza Cárdenas, 60, the mother of José Luis Olivo, who disappeared two years ago and is believed to be buried nearby. "Here, if you talked, you died."

The fear began to dissipate this year after a hard-charging colonel, Rafael Colón, was given command of the local marine base, residents said. Rooting out paramilitary forces as zealously as they did Marxist rebels, the marines instilled a sense of order the region had never known.

That prompted one family, the Verbels, who knew about the graves to come forward. "Here, everyone knew about the graves, and we reported them," said Hermés Verbel, 43, one of eight brothers who organized the villagers. "Everyone knew how the paramilitaries took land, took people's cattle."

For their daring, the Verbel family paid a high price: the killing of one of the brothers, Guillermo, 52, in January. But by then the death only energized villagers. More came forward.

Maruja del Carmen Pestana lost two sons, and Hermenijirda Julio said her son, Jairo Luis Alta Miranda, was grabbed by gunmen from the local bullfighting ring in 2003.

For now, the authorities are searching for graves with the help of the families of the victims and informants like Feliciano Yepes, a former paramilitary commander now in prison. He has led investigators to one grave after another.

Jenny Carolina Gonzalez contributed reporting from Bogotá for this article.