Somalia’s Internal Split: A Growing Threat to the War on Al-Shabaab

MOGADISHU, Somalia – The fragile unity of Somalia’s security apparatus is facing a critical test as a bitter standoff between the federal government and South West State threatens to overshadow the country’s long-standing war against Al-Shabaab.

At the heart of the crisis is a stunning allegation from officials in Baidoa, the interim capital of South West State. The regional administration claims it has "irrefutable evidence" of a dangerous "integration" between Al-Qaeda-linked militants and the Somali federal government.

The spark for this latest firestorm was the reported movement of federal military officers and heavy equipment through insurgent-held "red zones" between Baidoa and Burhakaba. Regional leaders argue that the lack of combat during this transit is proof of a "safe passage" agreement—a move they have formally labeled a "threat to national security."

"When federal forces move freely through territories controlled by those they are supposed to be fighting, it raises questions that strike at the very heart of our national stability," a senior South West State official said, speaking on condition of anonymity.

The timing could not be worse for President Hassan Sheikh Mohamud’s administration. As the African Union prepares to transition its security responsibilities to a new mission, the "AUSSOM," the cohesion of Somalia’s internal federal-member state relations is essential.

However, the political landscape is increasingly fractured. South West State’s allegations follow similar patterns of defiance from Puntland and Jubbaland, forming a "federalist bloc" that accuses Mogadishu of using the national army to settle political scores rather than fighting terrorists.

In Djibouti, the Intergovernmental Authority on Development (IGAD) issued a sharp plea for "restraint" on Sunday. The regional bloc, which counts Somalia as a founding member, expressed "deep concern over rising tensions" and urged all parties to utilize "inclusive dialogue and established national mechanisms" to resolve the rift.

"IGAD reaffirms its commitment to supporting Somalia’s peace, stability, and unity," the statement read, offering to facilitate formal reconciliation.

The escalating rhetoric represents more than just a political disagreement; it is a tactical nightmare. If the trust between the regional "Darwish" paramilitary forces and the Somali National Army (SNA) collapses, the vacuum created will almost certainly be filled by Al-Shabaab, reversing years of hard-won territorial gains.

As the Somali people watch with mounting anxiety, the question remains whether Mogadishu and Baidoa can find a path back to the negotiating table before the "national security threat" they describe becomes an irreversible reality on the battlefield.

On Saturday, March 28, the Southwest state parliament voted overwhelmingly to re-elect incumbent Abdulaziz Lafta-Garen during an indirect election in Baidoa city, a vote that the Federal Government has rejected as illegitimate. Following the election, Federal forces moved closer to the city amid efforts to remove the regional leader who has been in office since 2018 from power.

By Omar Nor, a veteran Somali journalist with nearly two decades of experience. He is widely recognised for his reporting and analysis on the Horn of Africa, particularly regarding security, military developments, and federal-regional political disputes. @Omaarnor

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