Abdullahi Mohamed Ali will replace Mahad Mohamed Salad as the head of the National Intelligence and Security Agency (NISA), it said.
No reason was given for the change, but the appointment comes a few weeks after a bloody two-day attack in March on a popular hotel in a highly secure neighbourhood of the capital Mogadishu.
Al-Qaeda-linked Al-Shabab group, which has been waging a deadly insurgency against the fragile central government in Mogadishu for more than 16 years, claimed responsibility for the attack.
Ali "has vast experience in running tasks related to the national security and intelligence," the cabinet said in a statement.
He has served in various government positions, including as minister and ambassador.
Also known as Sanbaloolshe, he previously headed NISA between July and September 2014 during the first term of current President Hassan Sheikh Mohamud, and later from April to October 2017.
Salad, who was appointed in August 2022, confirmed his departure in a statement and sent his "congratulations" to his successor.
Last month, NISA said it had arrested 16 people, including five members of security agencies, suspected of being involved in the hotel attack that claimed three lives.
The hotel siege broke a relative lull in attacks by Al-Shabab militants in the face of a major offensive against them launched in 2022 by government forces and local clan militias.
Although Al-Shabab was driven out of the capital by an African Union force in 2011, it retains a strong presence in rural Somalia and has carried out numerous attacks against political, security and civilian targets.
The jihadists have often targeted hotels, which host high-ranking Somali and foreign officials.