Al Shabaab’s close ties to Somalia government and threat to regional security

In Summary

• The terrorist group has allegedly infiltrated the FGS and the Federal Member States (FMS). 

KDF soldier disembarks from KNS Jasiri during capture of Kismayo
KDF soldier disembarks from KNS Jasiri during capture of Kismayo
Image: KDF

A recent media report revealing a relationship between al Shabaab and the National Intelligence and Security Agency of Somalia (NISA) was met with praise and criticism – praise for unearthing what some critics have called an open secret about the financial and material support, and criticism by the Somali government that the report was an attempt to dent its image.

However, it appears the report has opened a Pandora’s box as more incriminating information has emerged about links between al Shabaab, NISA and the Federal Government of Somalia (FGS). Security sources say the influence al Shabaab exerts over the government is unprecedented.

The terrorist group has allegedly infiltrated the FGS and the Federal Member States (FMS). Its members occupy key positions, enabling Shabaab to receive financial support and influence decision-making. It is why the terrorist group has upscaled attacks in Somalia and the region, particularly in Kenya.


Clan elders determine political representation in Somalia. Al Shabaab has been coercing them to select candidates who are friendly to their ideology. Through this, the group has links with MPs at all levels and uses them to lobby for the appointment of its sympathisers and financiers into the Cabinet.

Analysts say al Shabaab's inroads in government point to its long-term plan to ascend to power and create an Islamic caliphate in Eastern Africa. Within Somalia, the group has set up a quasi-government that collects taxes, runs schools and adjudicates disputes. Experts say it has established parallel administrative structures in five of the seven federal states, including the capital, Mogadishu.

Within the states, Shabaab militants collect taxes, especially in south-central Somalia and Benadir, where the FGS has little control. Its spies scare away FGS tax collectors, denying the government millions in revenue.

They have erected roadblocks in major supply routes and penetrated the management of major seaports to impose their taxes.

Mohamud Abdi (name changed to protect his identity), a former seafarer in Mogadishu, is now based in Mombasa after fleeing.

“We could not take our boats out to the sea without the permission of the militants. And when we went, you paid a specific amount of money for them to let you out. And when you came back, you would still find them at the port waiting for you to give them a share of your earnings before they let you disembark,” he said.

When asked why they did not report this to the government, Abdi simply quipped, “There is nothing that they can do. Al Shabaab has now become [like] the government.”


No industry has been spared al Shabaab’s appetite for money. NGOs, land and real estate dealers, construction, farmers and even herders pay tax to be allowed to operate.

Security experts believe the rise to power of al Shabaab was facilitated by someone close to power in Somalia. For some, the middleman is Fahad Haji Dahir Yassin, current director general of NISA. Yassin is one of the most influential figures in Somalia and a close confidant of President Mohammed Farmajo. It is even intimated that he had a hand in Farmajo’s election.

Yassin rose to power from a trainee militant in the early 1990s, and an obscure spy in the 2000s, to become among the most influential people in Somalia. He trained as a combatant in Afghanistan and Pakistan alongside prominent al Shabaab leaders Hassan Dahir Aweys and Ahmed Abdi Godane, now deceased.

He later became a member of Al-Itihad Al-Islamiya (AIAI) - also known as the Islamic Union - a militant Somali organisation with ties to al Qaeda - until 1997, when he enrolled for a degree in religious studies at Al-Iman University in Sanaa, Yemen.

Years after his studies, Yassin was hired by Qatar state-funded Al Jazeera. In 2006, he was appointed head of the Somalia bureau, where he worked until he joined the country’s security.

However, Yassin never abandoned his militant tendencies. From this period to 2012, it is alleged he was an undercover operative for Qatar and Ethiopia.

In 2012, he supported the candidature of Hassan Sheikh Mohamud by channeling to him campaign funds from Qatar. When Mohamud became the eighth president of Somalia, he rewarded Yassin with the appointment as Minister for Port and Marine Transport. However, this was short-lived as Yassin resigned over suspected connections to al Shabaab.

Yassin and Mohamud disagreed in 2016 and he shifted Qatar's political sponsorship to Mohamed Farmajo, who won the presidency in 2017. For his reward, he was appointed in 2018 the director general of NISA.

He reorganised the institution that had previously investigated him and declared him unfit for public office. Yassin recruited politically inclined security and intelligence personnel from extremist groups and established NISA as a conduit for funding, mainly from Qatar.

It is believed Qatar has been channeling millions of dollars to Somalia to create a loyalist administration to counter growing Turkish and UAE influence. 

Yassin uses Qatar’s funds to weaken the Somali government.


On the other hand, he has been able to somewhat control the terror group. In May 2018, it was reported he offered $1.8 million to Abdirahman Mohamed Warsame alias Mahat Karate, deputy Shabaab leader, to halt attacks during Ramadhan.

Other briefs to al Shabaab are said to include carrying out attacks targeted at Turkish expatriates in Somalia. Such attacks have slowed down Turkey’s projects in the country as well as those by other countries, including the stalled modern port at Berbera by the UAE.

Aside from financial support, Yassin has been denigrating the Amisom forces to push for their withdrawal from Somalia. NISA and FGS have allegedly been issuing misleading coordinates for precision attacks to both the Amisom and the US-led Africa Command Forces to ensure they miss their targets to increase negative publicity.

Following the recent maritime dispute between Kenya and Somalia, the tussle over Jubaland and the stalemate over the border wall Kenya is building Kenya has been branded an enemy of Somalia, a narrative Yassin, NISA and al Shabaab are keen to exploit.

Other Amisom contributing countries have also been disparaged via negative propaganda from some Somali citizens and diaspora communities, which share Yassin’s view.

Owing to this antagonistic view of Kenya, NISA has been actively sponsoring al Shabaab leadership to attack and frustrate KDF and Amisom operations to pile pressure on Kenya to withdraw from Somalia.

It is reliably reported that Yassin is not the only high-ranking Somali leader connected to Shabaab. His deputy, Abdullahi Kulane alias Jiis Marihan, is also an ardent al Shabaab supporter.

Security experts warn that with Yassin exercising undue influence over the president and prime minister of Somalia, and with help from countries such as Qatar, it is only a matter of time before he attains his goal of establishing an Islamic caliphate in Somalia - especially if he manages to frustrate countries like Kenya and Amisom partners trying to get Somalia back on its feet.