Serious issues involving human rights in Honduras through the end of 2013 include unlawful and arbitrary killings by police and others, corruption and institutional weakness of the justice system, and harsh and at times life-threatening prison conditions.
Seven former members of Battalion 3-16 (Billy Joya, Alvaro Romero, Erick Sánchez, Onofre Oyuela Oyuela, Napoleón Nassar Herrera, Vicente Rafael Canales Nuñez, Salomón Escoto Salinas and René Maradianga Panchamé) occupied important positions in the administration of President Manuel Zelaya as of mid-2006, according to the human rights organisation CODEH.
This suspended civil liberties including freedom of transit and due process, as well as permitting search and seizure without a warrant.
[20] Amnesty International (AI) stated that during the Micheletti period, "increasingly disproportionate and excessive use of force [was] being used by the police and military to repress legitimate and peaceful protests across the country".
AI also said that "some women and girls taking part in the demonstrations are reportedly suffering gender based violence and abuse at the hands of police officers" and that at the same time that "protests increase and spread throughout the country, violent methods of repressing dissent intensify and Honduran citizens are increasingly exposed to violations of their fundamental rights.
"[10] On 5 July, in San Juan Pueblo, Atlántida, four people wearing police vests forcefully disappeared Anastasio Barrera, 55 years old, of the National Union of Rural Workers.
[25] On 3 July in Tegucigalpa, Alexis Fernando Amador, 25 yrs old, was found dead in a blue plastic barrel with mortal wounds in his head, wearing a T-shirt referring to the "cuarta urna" (Fourth ballot box) that might have been voted on in the poll relating to organising a constituent assembly in Honduras.
[25] Also on 3 July, journalist Gabriel Fino Noriega who had expressed opinions in favour of the project to hold a constituent assembly in Honduras and against the coup d'état,[24] was killed by 7 bullets when he left his workplace.
On 9 July at 11:30 in the morning, Jose David Murillo was detained by Direccion Nacional de Investigacion Criminal (DNIC) agents when he left the offices of COFADEH.
[20] Images of Isis Obed Murillo's bloodstained body were widely circulated and became a focal point for people opposed to the coup d'état.
[27][28][29] Roger Iván Bados (sometimes written Báez[30]), a former union leader, who had become a member of the Democratic Unification Party and the Popular Bloque (BP), was "threatened with death immediately after the coup" and shot dead on 11 July next to his house in San Pedro Sula.
[22] According to Dr Luther Castillo of the Garifuna community organisation Luaga Hatuadi Waduheñu Foundation, the assassination "can be directly attributed to" the Micheletti's de facto government.
[21] The death of 40-year-old campesino leader Ramón García, also a member of the Democratic Unification Party, on 12 July, after he was forced by unknown people to get off a bus,[20] is also attributed to Micheletti's de facto government by Luther Castillo.
[22][30] On 24 July, near the border town El Paraíso, conflict occurred between hundreds of protesters against the coup d'état and security forces.
"[32] On 31 July, during a peaceful protest that blocked a highway on the first day of a public service national strike against the coup d'état, high school teacher Roger Abraham Vallejo Soriano, 38 years old, was shot in the head by security forces.
[36] Another assassination in the region near the Nicaraguan border near El Paraíso took place on 2 August when a soldier at a military roadblock fatally shot Pedro Pablo Hernández in the head.
[40] On 16 October 2009, Human Rights Watch stated that "the small human rights unit of the Office of the Attorney General has begun investigations into numerous cases of killings, alleged excessive use of force by security officials, and illegal and arbitrary detentions" but that the unit's superiors in the Attorney General's office and armed forces members were obstructing the investigations.
[46] In December 2009 the head of Honduras' anti-drug smuggling operations, Gen Julian Aristides Gonzalez, was assassinated in Tegucigalpa,[47] as was anti-coup activist and LGBT rights leader Walter Trochez.
"[48] Journalist David Meza was assassinated in March 2010; he investigated drug trafficking within Honduras, and reportedly received death threats in 2010, according to the El Tiempo newspaper.