Uganda said on Monday it had begun withdrawing its troops from Somalia as part of a phased drawdown that will end an almost two-decade deployment helping Mogadishu fight the al Qaeda-linked al Shabaab insurgency.

Uganda has about 4 500 troops deployed in Somalia under the African Union-mandated AU Support and Stabilization Mission in Somalia (AUSSOM), according to state media, though it is unclear how many additional forces are deployed under a separate bilateral arrangement.

The first troops to leave are those deployed under the bilateral arrangement, Uganda People's Defence Forces (UPDF) spokesperson Chris Magezi said in a statement.

"UPDF has embarked on the drawdown of troops deployed in Somalia under bilateral arrangements with (Somalia's) Federal Government, effective immediately," Magezi said, adding that the first cohort had already returned home.

Uganda will gradually withdraw all its forces from Somalia, including those serving under AUSSOM, by the end of 2027, he said.

In an October 31 letter from AUSSOM to the UN Support Office in Somalia, verified by two diplomatic sources, the mission warned the withdrawal could leave parts of the Lower Shabelle region vulnerable to al Shabaab attacks.

Ali Omar, Somali state minister for foreign affairs, told Reuters: “Things are not dire now, but it could create problems if their troops suddenly pull out”.

Al Shabaab has waged an insurgency against Somalia's government for about two decades, seeking to seize power and impose its strict interpretation of Islamic law.

The group continues to carry out bombings and gun attacks against military and civilian targets.