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The outgoing president Farmajo was accused of being the main obstacle to the country's elections as he is seeking to hijack the process.
The ex-NISA chief is the prime suspect in the murder case of senior intelligence officer Ikran Tahlil that sparked the worst political crisis in Somalia.
On Thursday, Farmajo released a statement announcing that he suspended the executive PM’s powers to sack or dismiss government officials during the elections, a move that has fueled the brewing tension.
The outgoing president has taken yet another dangerous measure to create instability and battle over power in the Horn of Africa country.
The commander of the Turkish-trained special police known as Haram'ad was among those wounded in the confrontation in the capital.
The outgoing president proofed his intentions to save Fahad Yasin and his close circles from prosecution over the murder of the senior NISA female agent.
Heavily armed rival forces were spotted around the NISA HQs on Wednesday morning amid reports of attempt by new security minister to arrive there.
The PM warned Farmajo against any attempt to derail the ongoing investigation by the military court which is expected to release its findings on Thursday, September 15, according to Keydmedia sources.
The blast is the second since last April in the same vicinity as Al-Shabaab intensifies attacks against Somali military bases.
Speaking to the media in Mogadishu, the bereaved mother said the family has confidence only in the committee appointed by PM Mohamed Hussein Roble to probe the case.
The country's PM has already appointed an inquiry body to look into the reported murder of Ikran Tahlil went missing last June in Mogadishu.
The former Al-Shabaab deputy leader and spokesman has been on house arrest in Mogadishu for three years and his life came in danger from Fahad Yasin.