Kenya's Patience with Mogadishu Wears Thin
On 18 January, a Kenyan aircraft delivered Jubaland President Ahmed Islam Madoobe from Kismaayo to Nairobi to allow him to travel to the UAE on health grounds. Defying a federal aviation ban imposed on Kismaayo, the private Kenyan plane did not seek clearance from Mogadishu's Traffic Control Centre and switched off its transponders when it crossed into Somali airspace. In turn, Somalia's Foreign Ministry promptly protested, terming it a breach of its airspace and sovereignty, summoning the Kenyan ambassador and threatening to recall its own representative in Nairobi. The flight has now tipped delicate bilateral relations between the neighbours into a tailspin.
The Jubaland strongman frequently travels to Nairobi and the Gulf state for specialised treatment. In the past month, however, Madoobe has been marooned in the port city and unable to travel owing to a punitive aviation ban imposed by Villa Somalia on the regional administration. Since the Ras Kambooni debacle and the routing of several hundred Somali National Army (SNA) troops in December, Madoobe has been battling attempts to disrupt his administration in Gedo. But with his position as Jubaland president in Kismaayo largely secured, Madoobe may be returning to his typical international schedule of recent years. The leader is also expected to meet with senior Kenyan officials and foreign diplomats while in Nairobi. Jubaland recently announced it would seek to develop independent international relations with partners like Puntland.
The decision by Kenya to defy the aviation ban and airlift Madoobe further suggests that Nairobi is shifting against that of Mogadishu and the Hassan Sheikh administration. One senior diplomat told Sahan Research that "this is Ruto telling HSM, 'I am fed up and don't care.'" Given the years of strategic Kenya-Jubaland relations, Nairobi feels it owes Madoobe a 'duty of care,' and has been dismayed by Villa Somalia's decision to aggressively militarise its dispute with the Jubaland president and impose an aviation embargo. This embargo has also been roundly ignored by another of Somalia's neighbours-- Ethiopia, which has delivered several caches of weapons and advisors to Kismaayo. The inability of Somalia's federal government to enforce the aviation ban on its neighbours has only underlined the frailty of Mogadishu.
The current spat comes in the face of two years of steady improvement of Mogadishu-Nairobi relations. In particular, Kenya played an instrumental role in fast-tracking Somalia's entry into the East African Community, even though Mogadishu is irked that its citizens still do not enjoy visa-free travel to Kenya. Amid the downturn of Ethiopia-Somalia relations, Nairobi has kept largely on the sidelines, repeatedly offering to mediate between Somali President Hassan Sheikh and Ethiopian PM Abiy Ahmed. And Somalia's political elite still love Nairobi, with many preferring to keep their families in the city than in Mogadishu. Following the SNA's defeat by Jubaland Daraawiish in December, Kenya even airlifted dozens of disarmed Gorgor troops that had fled over the border back to Mogadishu.
In late 2024, Hassan Sheikh requested Kenya's help in mediating the dispute between Mogadishu and Kismaayo. Kenya's influential Director-General of the National Intelligence Service (NIS), Noordin Haji, Amb Mohammed Affey and Amb Mahboub Maalim, were dispatched to both cities to broker a compromise solution. This attempt failed, in large part because Hassan Sheikh was more invested in scuttling Madoobe's electoral agenda than resolving the causes of the perennial disputes with Jubaland. Other proposals from senior Kenyan officials that Madoobe could stand aside after a year were roundly dismissed by PM Hamza Abdi Barre, the Ogaadeen leader and once close ally of the Jubaland president. Instead, deploying forces to Ras Kambooni, imposing a draconian aviation ban and orchestrating a crisis in Gedo have all been interpreted as 'overreach' by Nairobi. Intercinine political disagreements taking precedence over targeting Al-Shabaab, which remains on both sides of the Jubaland-Kenya border, has further frustrated Kenya.
Yet Nairobi's attitude to Madoobe is complex and varied. Inter-agency friction in recent years has undermined the emergence of a clear and coherent policy on Jubaland. The Department of Defence, which has an enduring strategic relationship with Madoobe, prefers the status quo on the grounds that the regional leader offers Kenya a trusted, coherent, and predictable partnership. In late November, the Kenyan and Ethiopian militaries agreed on a Memorandum of Understanding (MoU) to combat Al-Shabaab in Somalia, which was then widely regarded as a vote of support for Madoobe. The NIS, meanwhile, in the last two years, has become influenced by powerful Ogaadeen leaders seeking to oust Madoobe. Mogadishu's hostile and active destabilisation of Jubaland in recent weeks, however, has gelled the Kenyan agencies and restored the old paradigm of prioritising the Jubaland relationship over Somalia's central government.
For Villa Somalia, any ally-- no matter who-- of Madoobe remains fair game despite the costly fallout at Ras Kambooni. Having assumed a UN Security Council non-permanent member seat and hawkish Foreign Minister Ahmed Fiqi still in place, Mogadishu’s instinct to act tough with its neighbours may now be strengthened. Yet, while Mogadishu needs both Ethiopia and Kenya if the chaotic African Union Support and Stabilisation Mission in Somalia (AUSSOM) is not going to be an abject failure, it is still preferring internal domestic political wrangles over national security. The ongoing negotiations between Ethiopia and Somalia over the Ethiopian National Defence Force (ENDF) troop deployment in AUSSOM and bilaterally have included demands by Villa Somalia for Addis to suspend its relations with Somalia's regional administrations, as well as withdraw forces from Gedo. Though the Turkish-driven tentative detente remains in place, Addis has so far refused both conditions. Hassan Sheikh is also due in Cairo this week, ahead of Turkish President Recep Tayyip Erdoğan's visit, an act that may not sit well with Addis.
Until now, Kenya has been reluctant to pressure the Somali president to end his hostility towards Madoobe. Assuming Nairobi is now willing to play hardball with Mogadishu, more pressure tactics may soon be deployed and increase the likelihood of Kenya and Ethiopia closing ranks against Somalia. For Kenya, this could include visa restrictions, stalling on meeting requests, and blocking investment by Somali politicians. There are other pressure points as well, including the contested waters off Jubaland, where the Turkish research vessel, the Oruç Reis, is gathering 3D research on oil and natural gas. Picking another fight with another neighbouring state-- a close ally and critical for national security-- over a flight is just the latest piece of self-sabotage by Somalia's federal government.
The Somali Wire Team
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Two days of heavy clashes (3–4 June) in the Somali capital, Mogadishu, between federal troops and opposition-aligned forces have underscored both the fragility of the city’s security environment and the volatility of electoral politics. Although relative calm has since returned to the two hardest-hit districts - Hawl Wadaag and Abdiaziz - and mediation efforts have intensified, tensions remain high, fuelling fears of renewed armed skirmishes. Credible reports of mass clan militia mobilisation on the edges of Mogadishu speak to a conflict that is widening. The militarisation of politics and elite fragmentation over the electoral process have shattered a core assumption: that Somali leaders will ultimately step back from the brink to negotiate a way forward. Consequently, the country is entering a perilous phase in which domestic factions alone cannot resolve the impasse, making neutral, external mediation a necessity.
Puntland President Sa'id Abdullah Deni is unofficially in the race for the federal presidency of Somalia. By most accounts, the regional leader is running again and this explains his re-engagement with Mogadishu after a three-year hiatus. Driven by shifting electoral dynamics, Deni’s decision to re-engage with the centre forces him to confront a radically altered political landscape in Mogadishu. Under President Hassan Sheikh Mohamud (HSM), the federal government has rewritten the rules of Somali politics, altering the institutional framework and consolidating executive authority.
On 10 May, the Federal Government of Somalia (FGS) unilaterally conducted its contentious 'one-person-one-vote' (OPOV) electoral model in South West State (SWS), directly overriding opposition demands for a negotiated, consensus-based framework. Crucially, the very laws underpinning these OPOV elections are themselves deeply contested: the electoral framework was created following a rushed revision of Somalia’s constitution that many federal member states and opposition groups rejected. The vote, exclusively managed by the National Independent Electoral and Boundaries Commission (NIEBC), saw localised polling in 13 districts and across 126 poll centres and 276 stations. While 376,212 citizens were registered, actual turnout reached 132,430 voters - a participation rate of approximately 35.2% - with 128,276 valid ballots cast and 4,154 deemed spoilt/invalid. The electoral outcome, unsurprisingly, solidified a decisive mandate for Hassan Sheikh Mohamud’s Justice and Solidarity Party (JSP); the governing party secured an absolute majority of 51 out of 95 contested legislative seats, comfortably outpacing its closest rival, Sharif Hassan Sheikh Aden’s Ururka Horumarka, which claimed 14 seats.
The Federal Government of Somalia (FGS) has effectively entered a 'grey transition' - a deeply fraught and hotly-contested interregnum that could upend decades of state-building and foment greater instability. By utilising the March 2026 constitutional amendments to extend his presidential mandate until May 2027, Hassan Sheikh Mohamud (HSM) has effectively plunged the fragile Horn of Africa state into a profound period of severe internal strain and legitimacy crisis. This legalistic manoeuvre has roiled domestic politics and put Western partners of Somalia in a difficult spot. If Somalia's Western allies concede to HSM's fait accompli without extracting concessions from him on a negotiated settlement, they are likely to embolden Hassan Sheikh.
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