The agency was established in January 2013 by the new Federal Government of Somalia in place of the defunct National Security Service.

[8] Alpha Group is Gaashan's first component, and includes around 40 soldiers and 3 officers who were chosen from amongst 190 special Somali National Army troops.

Derek Gannon said that the Alpha Group's training regimen includes counter-insurgency, counter-terror operation and executive-protecting, with an emphasis on quick reaction in an urban environment.

[12] According to Ali, since Yasin was appointed to head NISA operations have focussed on silencing political opposition and criticism rather than overcoming Al Shabaab.

[14] In April 2020 NISA was accused of intimidation and harassment of Harun Maruf, a journalist who works with Voice of America, through Twitter.

In July 2021 Prime Minister Mohammed Hussein Roble dismissed head of NISA at Mogadishu's Aden Abdulle Airport Abdiwahab Sheikh Ali and NISA Chief of staff, Abdullahi Kulane after they refused to allow a group of passengers to fly from Mogadishu airport.

On 26 June 2021, NISA employee Ikran Tahlil Farah was abducted close to her home in Abdulaziz district of Mogadishu.

[19] Prime Minister Roble asked Director General of NISA, Fahad Yasin to submit a report on Ikran's death.