KISMAYO, Somalia – A deepening political conflict between Somalia’s federal government and the semi-autonomous state of Jubaland is creating a dangerous security vacuum, allowing Al-Shabaab militants to regain ground and forcing tens of thousands of civilians from their homes, according to officials and security experts.

Recent deadly clashes in the strategic Gedo region have laid bare severe fractures in Somalia’s fragile federal system, diverting attention and resources from the fight against the Al-Qaeda-linked extremist group. The violence comes as the country prepares for a contentious national election scheduled for next year.

Last week, fighting between Mogadishu-aligned federal forces and troops loyal to Jubaland’s administration left at least two soldiers dead. It followed earlier clashes in July that killed five, as both sides massed troops in a tense standoff over control of Gedo.

Analysts warn that such infighting offers a lifeline to Al-Shabaab. The group, which has battled the Somali state for nearly two decades, has already taken advantage of the distraction to retake several major towns this year, undoing years of hard-won progress.

“Once the attention shifted from the fight against Al-Shabaab to politics, we started seeing losses and setbacks on the battlefield,” said Samira Gaid, a Horn of Africa security analyst. She added that the Islamist insurgents are exploiting the power struggle as a “recruitment drive.”

A struggle for Gedo

At the heart of the crisis is a long-running feud between President Hassan Sheikh Mohamud and Jubaland’s leader, Ahmed Madobe. Relations collapsed last year after Madobe — a former warlord who has ruled the southern state since 2013 — secured a third term in an election that Mogadishu dismissed as “unlawful.”

The dispute has crystallized around the Gedo region, which borders Kenya and Ethiopia. Both Mohamud and Madobe are seeking to control the area ahead of the 2026 elections.

President Mohamud has pushed for a historic shift from Somalia’s clan-based indirect voting system to a direct, one-person, one-vote election — a reform Madobe strongly opposes.

“The reason why this is spiking now is because we are heading into the election,” explained Omar Mahmood, a senior analyst with the International Crisis Group. “Both leaders want to exert control over Gedo, which they can then use to influence the election process.”

Last month, tensions escalated further when Mohamud appointed Abdirashid Hassan Abdinur, widely known as Janan, to lead security operations in Jubaland. Janan, once Madobe’s security minister, is a powerful figure in Gedo but has been accused by the United Nations of serious human rights abuses, including obstructing humanitarian relief.

After last week’s clashes, Janan announced that his forces had seized control of the border town of Beled Hawo and declared a new administration would be formed — a direct challenge to Madobe’s authority.

Deep-seated tensions

The struggle underscores the weaknesses of Somalia’s federal system, created in 2012 to unify the country after decades of civil war. The arrangement divided Somalia into five member states — Puntland, Jubaland, Galmudug, Hirshabelle, and South West — whose relations with Mogadishu often remain strained.

“There wasn’t enough political agreement at the time of the formation of the Somali federal government,” Mahmood said, pointing to the “constant struggle and tension within the federal model.”

Clan politics further complicate the standoff. Gaid noted that the dominant clan in Gedo has long felt sidelined under Madobe’s rule, a grievance Mogadishu now seeks to exploit. Yet opposition to Madobe is fragmented, and federal backing is uncertain.

Local leaders also question the central government’s motives. “We are hearing that the federal government is trying to annex Gedo from the rest of the Jubaland-administered territories,” said Mohamed Jumale, a traditional elder in Jubaland. “It will not work.”

Meanwhile, civilians continue to pay the price. Humanitarian agencies report that clashes in Gedo since June have displaced 38,000 people within Somalia and driven another 10,200 across the border into Kenya — worsening an already dire humanitarian crisis in the Horn of Africa.