Despite international support, including transfers of weapons and ammunition by the USA, and the training of TFG troops by states including France, the TFG struggled to integrate and enlarge its security forces. On 23 December, the UN Security Council imposed sanctions, including an arms embargo, on Eritrea, accused of supporting Somali armed groups in violation of the UN arms embargo on Somalia. The UN Security Council continued to request the UN Secretary-General to plan for the relocation of UN operations into Somalia and for an eventual UN force.
Human rights abuses, including recruitment of children into armed forces, were raised in reports by the UN Secretary-General, the UN Independent Expert on Human Rights in Somalia, and the Representative of the UN Secretary-General on internally displaced persons. International and local calls to end impunity for crimes under international law did not translate into concrete steps by the TFG or the international community to establish a commission of inquiry into such crimes.
Hijacking of ships and kidnapping of maritime crews by pirates increased and expanded far beyond the Gulf of Aden, despite international naval patrols and renewed commitment by the Puntland authorities to try pirates. The Puntland authorities faced more insecurity, including killings of officials and civilians. Among those killed were five Pakistani Muslim clerics in Galkayo in August.
All parties to the conflict used mortars and heavy weapons in areas populated or frequented by civilians. Mogadishu civilians were particularly affected, as armed groups launched attacks from residential areas, and the TFG and AMISOM allegedly fired indiscriminately in response. As a result, numerous civilians were killed and injured.
- On 2 February, at least 10 civilians were killed and a dozen injured on Maka al-Mukarama road in Mogadishu when AMISOM soldiers allegedly opened fire after an explosion targeted their vehicle. The results of an AMISOM investigation into the incident were not publicly available by the end of the year.
- On 17 June, a mosque in the Karan district in northern Mogadishu was hit by a mortar at dusk after a day of fighting between the TFG, AMISOM and armed groups. Thirteen worshippers leaving after prayers were killed.
- On 11 September, the Martini hospital for disabled war veterans and a prison were hit by mortars during an attack by armed groups on the Mogadishu port. At least 11 people, including three children, were killed in the hospital. Four guards in the prison were killed and a dozen people were injured. Armed groups denied responsibility for the shelling.
Fighting and insecurity were a major cause of displacement. In January, fighting between al-Shabab and Ahlu Sunna Wal Jama'a in Dhusamareb and Guri El in central Somalia displaced 50,000 to 80,000 people.
The UN estimated that after the armed groups' offensive against the TFG in Mogadishu in May, over 255,000 people fled the capital, including 65,000 who had returned since January hoping for improved security. Many joined previously displaced people along the Afgoye corridor outside Mogadishu, which by the end of the year hosted some 366,000 people in squalid settlements.
Civilians also fled to neighbouring countries; more than 50,000 crossed the border with Kenya to reach refugee camps in Dadaab. Others undertook dangerous sea journeys across the Gulf of Aden to reach Yemen. According to the UN, almost 32,000 Somalis arrived in Yemen in 2009; 309 Somali and other nationals died, including by drowning, during the journey.