Richard Karemire told Xinhua that phased withdrawal is in compliance with the African Union- and United Nations-approved reduction of 1,000 uniformed personnel serving under African Union Mission in Somalia (AMISOM) by the December 31 deadline.
Uganda has started withdrawing its troops from Somalia, where they have been fighting al-Shabaab terrorists for 10 years, the military said Thursday.
Some 20,000 soldiers are now serving as part of the UN-backed fight against Al-Shabaab in Somalia.
Uganda, which was the first country to send troops to Somalia in 2007, is the biggest contributor with more than 6,000 soldiers in the war-torn country.
It is unknown why the African countries and the African Union have chose to withdraw troops at this time.
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The US has already increased its troop numbers in the country to more than 500 and stepped up airstrikes - boosting its co-operation with the Somali military.
Other African countries such as Burundi and Kenya also contribute to the regional force.
But the Somali military has struggled to rid the country of Al Shabaab militants, and smaller and growing numbers of Al Qaeda-affiliated jihadists, despite being supported by the AU and the United States who continue to carry out air strikes against Al Shabaab.
The combined forces had managed to clear the capital Mogadishu, and large swathes of the countryside of Al Shabaab, but over the previous year or so the group has managed to resume large-scale attacks targeting the government, military and civilians, culminating in the more than 500 people killed in the capital in October during a twin bombing.
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