- Police use of excessive force and abuse of authority
- Perception of impunity
- Arbitrary arrest and detention
- An inefficient and understaffed judiciary that deprived citizens of due process and an expeditious and fair trial
- Conditions in camps for internally displaced persons (IDPs) that endangered health, security,
- education, and women's and children's rights.
- Domestic violence, rape and sexual abuse.
In an exchange of gunfire with armed rebels on February 11, President Ramos-Horta was wounded seriously and PM Kay Rala Xanana Gusmão was unhurt. As provided for in the constitution, the government imposed a state of emergency from February through May. International security forces in the country included the UN Police (UNPOL) within the UN Integrated Mission in Timor-Leste (UNMIT) and the International Stabilisation Force (ISF), neither of which was under the direct control of the government. The national security forces are the National Police (PNTL) and Defence Forces (F-FDTL). While the government generally maintained control over these forces, there were problems with discipline and accountability.The report says there were "no politically motivated killings during the year".
However, on February 11, F-FDTL guards shot and killed Major Alfredo Reinado and one of his followers when a band of rebels led by Reinado gained entry to the presidential compound; President Ramos-Horta was severely wounded. A separate group of Reinado's followers attacked the convoy of PM Xanana Gusmão. Gusmão was unhurt. The government formed a joint PNTL/F-FDTL command to apprehend the attackers, and Parliament declared a state of siege that imposed a curfew, relaxed legal requirements for searches and arrests, and restricted demonstrations. The application of the state of siege was modified as a state of emergency and extended on several occasions until Reinado's second in command, Lieutenant Gastao Salsinha, and 11 others surrendered to the authorities on April 29.Other incidents cited by the report included:
- On April 5, in Bobonaro District, an F-FDTL member shot and killed a civilian who reportedly threatened the F-FDTL member with a machete. The authorities investigated the case and forwarded it to the prosecutor general for further action.
- Legal proceedings were ongoing against Luis da Silva, an off duty officer accused of shooting a member of then candidate Xanana Gusmao's security detail at a political rally in Viqueque in June 2007.
- There were no developments in the inquiry into the August 2007 case of a PNTL unit firing into a crowd in Viqueque, killing two.
- The four F-FDTL soldiers sentenced to 12 years, 11 years, and 10 years for the 2006 killing of eight unarmed PNTL personnel were serving their sentences at the military prison at F-FDTL headquarters in Dili. A local human rights nongovernmental organisation (NGO) and government contacts expressed concern that there was no civilian oversight of the prison.
- The January killing of three men by Border Patrol Unit personnel.
- The May mob killing of a police officer in Ermera District; and
- The May killing of six people in a house set on fire by a mob.
Investigations into other cases stemming from the April-May 2006 violence continued. Some individuals identified for investigation in the 2006 UN Commission of Inquiry Report were subpoenaed to testify regarding their role in illegal arms distribution.
In May, 2008 President Ramos-Horta granted pardons to a number of persons including former interior minister Rogerio Lobato sentenced for illegally distributing weapons during the 2006 violence and Joni Marques, a pro-Indonesia militia leader, sentenced for multiple killings in 1999.