Somalia’s Federal-Puntland Rift Casts Shadow Over Counterterrorism Campaign

20 June, 2026

Tensions between Somalia’s Federal Government and the Puntland administration are intensifying amid concerns that political and security disputes could affect ongoing operations against Islamic State (ISIS) and Al Shabaab militants in northern Somalia.

Photo: The President and Prime Minister of the Federal Republic of Somalia, Commander Jimcaale, the North-East Leader and politicians from Puntland, Villa Somalia.

Puntland officials have accused the Federal Government of expanding its military presence in the region at a sensitive time, as local forces continue operations against extremist groups in Bari and surrounding areas.

According to Puntland authorities and political figures aligned with the regional administration, recent troop recruitment and deployments linked to the Federal Government have been viewed locally as an attempt to reshape security arrangements inside Puntland. Federal authorities have not publicly characterised the deployments in those terms.

The disagreement comes as Somali President Hassan Sheikh Mohamud appointed Jimale Jama as commander of the Somali National Army’s 54th Division, based in Garowe. The appointment has drawn criticism from Puntland-aligned figures, who argue that the move introduces additional political friction into an already tense relationship between Mogadishu and Puntland’s leadership under President Said Abdullahi Deni.

Critics of the appointment point to Jimale Jama’s previous involvement in political and security disputes within Puntland, including periods of confrontation linked to local electoral processes. Supporters of the appointment have argued that federal military appointments remain within Mogadishu’s constitutional authority.

Additional concerns have emerged over the reported presence of forces associated with the Puntland Security Force (PSF), as well as armed groups recruited from parts of Mudug and Bari regions, which some Puntland officials allege are operating under federal command structures. Those claims have not been independently verified.

This week, Puntland authorities announced restrictions on the movement of federal forces within the region, reflecting a broader deterioration in relations between Garowe and Mogadishu.

Security analysts warn that prolonged political confrontation could divert attention and resources away from counterinsurgency operations. Puntland has been conducting military efforts targeting ISIS fighters in the Al-Miskaad mountain areas of Bari region and has also discussed plans aimed at preventing Al Shabaab expansion into parts of the Sanaag region.

Observers note that Somali federal-regional tensions have previously coincided with periods of reduced coordination in security operations, creating concerns that militant groups could exploit political divisions.

The President of the Federal Republic of Somalia, Hassan Sheikh Mohamud in Baidoa. 3 April 2026

The current dispute also follows earlier federal involvement in political developments in South West State, where political competition surrounding regional leadership drew national attention and criticism from opposition figures.

Whether the latest tensions remain political or develop into a wider security confrontation may have broader implications for Somalia’s efforts to contain extremist groups and maintain coordination between federal and regional authorities.

Mohamed Osman
Horseed Media