- On 7 June, Mukhtar Mohamed Hirabe, director of Radio Shabelle, was shot dead by unknown gunmen in Bakara market. His colleague Ahmed Omar Hashi was injured in the shooting. Mukhtar Mohamed Hirabe was the third Radio Shabelle journalist to be killed and the second radio director to be murdered in 2009.
- On 1 October, the al-Shabab faction in Baidoa entered the premises of RadioWarsan, asked the station to stop broadcasting and detained two of its journalists for two days, reportedly accusing them of broadcasting music contrary to Islam. On 21 October, al-Shabab in Baidoa closed RadioWarsan and Radio Jubba.
- On 2 June, director of Somali Universal Satellite TV Ibrahim Mohamed Hussein was abducted by masked gunmen in the Afgoye district; he was released days later. Two foreign journalists, Canadian reporter Amanda Lindhout and Australian photographer Nigel Brennan, were freed on 25 November. They had been held hostage since their kidnapping in Afgoye on 23 August 2008. Two Somali men abducted with them were freed on 15 January.
- Between 19 and 21 August, armed groups looted the offices of a civil society organization in Mogadishu.
- On 2 November, al-Shabab reportedly closed three women's organizations in Beled Hawo in Gedo region, claiming that Islam does not allow women to work.
- On 3 December, a suicide bomber detonated explosives at a medical graduation ceremony in Mogadishu. The attack killed at least 23 people, including medical students, university staff, three journalists and three TFG ministers, and injured at least 56 others. No one claimed responsibility for the attack.
There was no effective functioning and centralized justice system in south and central Somalia. The UN Development Programme continued to provide capacity-building support for detention facilities, courts and police forces. The Office of the High Commissioner for Human Rights agreed with the TFG to provide technical assistance in human rights and support for the fight against impunity.
In Puntland, which had a functioning justice system, there were reports of arbitrary detentions and unfair trials.
Abuses by armed groups
Al-Shabab factions unlawfully killed and punished people they accused of spying or not conforming to their own interpretation of Islamic law. In areas under their control, there was an alarming rise in public killings, including stonings to death, as well as amputations and floggings. Al-Shabab factions also desecrated graves of Sufi religious leaders and put restrictions on women's dress and freedom of movement.
- On 25 June, Ali Mohamudi Geedi, Osmail Kalif Abdule, Jeylani Mohamed Had and Abdulkadir Adow Hirale had their right hands and left feet amputated by al-Shabab in front of a crowd in Suqahola in Mogadishu. They were accused of robbery.
- On 28 September, an al-Shabab firing squad publicly killed Mohamed Ali Salad and Hassan Moallim Abdullahi, whom they accused of spying for AMISOM and the US Central Intelligence Agency (CIA).
- On 16 October, al-Shabab forces in northern Mogadishu reportedly flogged women for wearing bras, claiming this was against Islam.
- On 7 November, Abas Hussein Abdirahman was stoned to death in front of a crowd in Merka. He was reportedly accused of a sexual offence.
- On 13 December, Mohamed Abukar was stoned to death in Afgoye by Hizbul Islam members. He was accused of sexual intercourse outside marriage with a woman, who was given 100 lashes.
The Republic of Somaliland, which declared independence in 1991, continued to seek international recognition, although Somaliland people focused their political attention on repeated delays in national elections. In late September, President Dahir Riyaale Kahin and two Somaliland opposition party leaders signed an agreement brokered by Ethiopian mediators to create a new election commission, fix a flawed voter registration list, and reschedule elections for 2010.