Richard Karemire blamed Sunday's attack on the radical Islamist group al-Shabaab, which more than 20,000 AU soldiers are fighting alongside government troops in the Horn of Africa country.
The Ugandans were attacked while carrying out a joint patrol with Somali soldiers between Goryowein and Beladamin at about 140 kilometres south-west of the capital, Mogadishu, Karemire told dpa.
Seven Ugandan soldiers were injured.
Al-Shabaab meanwhile put the number of AU fatalities at 39. They were all Ugandans, the group said Sunday on pro-insurgent radio Andalus.
Ugandan troops were now on the ground "to conduct counter-operations," the Ugandan Defence Ministry said in a statement.
It added that a board of inquiry would be constituted to establish the circumstances of the attack.
Somali officials declined to comment on the incident.
The US Africa Command meanwhile said the United States had killed one al-Shabaab fighter in a kinetic strike near Tortoroow in southern Somalia over the weekend.
"The US conducted this operation in coordination with its regional partners as a direct response to al-Shabaab actions, including recent attacks on Somali forces," the statement added.
Al-Shabaab militants. File picture
Somali militants have ambushed and killed 12 Ugandan troops serving under the African Union (AU) in Somalia, a Ugandan Defence Ministry spokesman said Monday.
