Opening the summit, Ugandan President Yoweri Museveni called for action to "sweep the terrorists' out of Africa.
And he blamed foreigners for the Kampala attacks, which the Somali-base al-Shebab group has said it carried out.
"Let them go back to Asia or the Middle East where I understand some come from," he said.
Museveni also said many of the organisers of the attacks in Kampala have been arrested and questioned.
"Their interrogations have yielded very good information," he added.
Mutharika declared the organisation's solidarity with Uganda.
"The African Union stands with you, my brother President Museveni, and with the people of Uganda," he said in his opening remarks.
The summit was supposed to concentrate on women, children and health but these questions have so far been overshadowed by the response to the Kampala bombings.
Museveni tried to allay fears by women and child rights activists here that the original theme of the summit was being put in the back seat as leaders grapple with Somalia, Sudan and reform of the UN Security Council," reports Billie O'Kadameri from the summit. "The theme chosen chosen for this summit is 'Maternal and Child Health and Infant Development in Africa' but Museveni said it was a narrow view of looking at the bigger problem.
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