"We discovered the lifeless bodies of 54 fallen soldiers, including a commander," Museveni said in a statement posted on his official Twitter account late Saturday.
Al-Shabaab, which has been waging a deadly insurgency against Somalia's fragile central government for more than a decade, claimed responsibility for the dawn attack on May 26.
The terrorists drove a car laden with explosives into the base in Bulo Marer, 120 kilometers (75 miles) southwest of the capital Mogadishu, leading to a gunfight, local residents and a Somali military commander told AFP.
The toll is one of the heaviest yet since pro-government forces backed by the AU force known as ATMIS launched an offensive last August against Al-Shabaab.
Museveni had already said last week that an initial panicked reaction to the attack contributed to the toll.
"The mistake was made by two commanders, Maj. Oluka and Maj. Obbo, who ordered the soldiers to retreat," Museveni said in the statement, adding that they would face charges in a court martial.
However, "our soldiers demonstrated remarkable resilience and reorganized themselves, resulting in the recapture of the base."
The 20,000-member ATMIS force has a more offensive remit than its predecessor, known as AMISOM.
The force is drawn from Uganda, Burundi, Djibouti, Ethiopia and Kenya, with troops deployed in southern and central Somalia.
Its goal is to hand over security responsibilities to Somalia's army and police by 2024.
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