Violence increased sharply around the time of parliamentary and presidential elections, creating a climate of fear and intimidation. There were reports that security forces used unnecessary or excessive force during demonstrations and tortured and illtreated people during arrest, questioning and detention. Security forces also reportedly committed unlawful killings. Severe restrictions were imposed on the right to peaceful assembly and expression.
- On 6 April, police opened fire on a protest in the city of Nabire, Papua province, injuring at least seven people including a 10-year-old pupil who was shot as he returned from school. A police officer was also injured by an arrow. Police beat and otherwise illtreated Monika Zonggonau, Abet Nego Keiya and fifteen other political activists during and after arrest. On 9 April, the body of Abet Nego Keiya was found at Waharia village, Nabire district.
- Prisoners of conscience Filep Karma and Yusak Pakage, sentenced to 15 and 10 years' imprisonment respectively, remained in jail. The two men were convicted in 2005 for raising the "Morning Star" flag.
Torture remained widespread during arrest, interrogation and detention. Criminal suspects from poor and marginalized communities and peaceful political activists were particularly vulnerable to violations by police, including unnecessary or excessive use of force, sometimes resulting in death; torture and other ill-treatment; and failure to protect demonstrators and religious minorities.
- In January, at least 75 villagers from Suluk Bongkal village in Riau province were charged with illegally claiming land. Police had arrested them in December 2008 after forcibly evicting them. In August, they were sentenced to 10 months' imprisonment and a fine of 1 million Indonesian rupiah. By the end of the year, the villagers had not received compensation, reparations or alternative adequate housing.
In January, the police issued a new regulation on the use of force in police action (No.1/2009), largely in line with the UN Basic Principles on the Use of Force and Firearms. In June, the police issued a regulation on the implementation of human rights principles (No.8/2009). However, internal and external accountability mechanisms to deal with police abuse remained weak.
Impunity for past gross human rights violations in Aceh, Papua, Timor-Leste and elsewhere continued. The government continued to promote reconciliation with Timor-Leste at the expense of justice for crimes under the Indonesian occupation of East Timor (1975-1999).
- In August, the government interfered with the judicial process in Timor-Leste by pressuring the Timor- Leste government to release Martenus Bere, an indicted militia leader charged with the extermination of civilians in the town of Suai and other crimes against humanity in 1999. In October, Martenus Bere was allowed to return to West Timor (Indonesia) before his case had been prosecuted by an independent court in a fair trial.
Over 300 individuals who were indicted by the UN Special Panels for Serious Crimes for crimes against humanity and other crimes remained at large and were outside the territorial jurisdiction of Timor-Leste. Most of them were believed to live in Indonesia. The government refused to facilitate the extradition of those indicted on the basis that it did not recognize the UN mandate to try Indonesian citizens in Timor- Leste.
In September, the Special Committee on Disappearances 1997-1998 of the House of People's Representatives urged the government to create an ad hoc human rights court to try those responsible for enforced disappearances. They also urged the government to ratify the International Convention for the Protection of All Persons from Enforced Disappearance. However, the government had not acted on the recommendations by the end of the year.
No executions were reported. However, at least 117 people remained under sentence of death.