The human rights situation deteriorated significantly after the return to civilian rule in 1982. Under the new civilian president, the military, under the command of General Gustavo Álvarez Martínez, initiated a campaign against leftists. This campaign allegedly led to the disappearance of more than 100 people. Small insurgent groups also began operating during this period, but the overwhelming majority of political killings were carried out by the military, according to human rights observers. Although this violence paled in comparison to that in neighboring El Salvador and Guatemala, it marked a departure from the relatively tranquil Honduran political environment.
Beginning in 1985, political violence declined significantly, but did not completely disappear; a small number of extrajudicial killings continued to be reported annually for the balance of the 1980s and early 1990s. In July 1988 and January 1989, the InterAmerican Court of Human Rights (IACHR) held the Honduran government responsible for the 1982 disappearances of a student activist, Ángel Manfredo Velásquez, and a secondary school teacher and union activist, Saúl Godínez. The IACHR also determined that Honduran authorities were responsible for a deliberate kidnapping campaign of between 100 and 150 individuals believed to be tied to subversive activities between 1981 and 1984.
In the early 1990s, as the political conflicts in El Salvador and Nicaragua abated, the Honduran public increasingly began to criticize the military for human rights violations. These violations allegedly included a number of political and other types of extrajudicial killings. One case in particular that ignited a public outcry against the military was the July 1991 rape, torture, and murder of an eighteen-year old student, Riccy Mabel Martínez, by military personnel. Initially, the military did not allow the civilian courts to try the three suspects, but ultimately the military discharged the suspects from the military so as to avoid the precedent of military members being tried in civilian courts. After a long, drawn-out process, two of the suspects, including a former colonel, were convicted of the crime in July 1993, marking the first time that a high-ranking officer, even though no longer in the military, was prosecuted in the civilian courts.
Observers credit former United States Ambassador Cresencio Arcos with speaking out promptly on the case and urging the Honduran government to prosecute it through an open judicial process. In fact, the United States embassy increasingly has been viewed as a champion for human rights in Honduras, and its annual human rights reports are considerably more critical than those prepared in the 1980s.
Nevertheless, the military's disregard for civilian authority is demonstrated by the military's immunity from prosecution for human rights violations. In early 1993, after considerable public criticism of alleged military involvement in the January 1993 killing of a San Pedro Sula businessperson, the military deployed forces in both San Pedro Sula and in the capital. Rumors abounded about the true intention of the deployment, reportedly made without the knowledge of President Rafael Leonardo Callejas Romero. Some observers speculated that the armed forces chief, General Luis Alonso Discua, took the action to intimidate his opponents and stem a barrage of recent criticism against the military. President Callejas later announced that he had ordered the deployment as one of a series of actions to deter criminal violence.
Some critics maintain that President Callejas should have been more forceful with the military and attempted to assert more civilian control during his presidency, particularly when the military tried to impede the prosecution of the Riccy Martínez case. Some maintain that Callejas himself had close ties with General Discua, thus explaining why no strong civilian action was taken against the military. Other analysts, however, maintain that Callejas substantially improved civilian control over the military with the establishment of such commissions as the Ad Hoc Commission for Institutional Reform, which recommended the breakup of the DIN and the creation of a new Department of Criminal Investigation (Departamento de Investigación Criminal--DIC) within the civilian government.
Data as of December 1993