The National Assembly Majority leader said Annan manipulated the results that saw Foreign Affairs CS Amina Mohamed lose the AUC chairperson post to Chad's Moussa Mahamat.
He said the Kenyan delegation had every reason to believe Annan, who mediated the 2007/8 post election crisis, influenced the Monday vote.
"A number of issues which were at play. I even saw a group of activists led by Kofi Annan at the ICC discrediting our candidate," he told journalists on Tuesday.
Duale also accused France, "which is fighting to recolonize Africa", of having a hand in the outcome. He said more than 15 heads of state abstained from the vote in a show of the country's influence.
He further questioned Morocco's comeback to the African Union and raised issues with Anglophone and Francophone relations.
The Star could not verify the claims by the majority leader, who spoke on Tuesday in Addis Ababa, Ethiopia, where the vote was taken.
But Amina earlier said Kenya's neighbours should be investigated for not supporting her election.
But Duale, who is also Garissa Town MP, dismissed claims that Amina's failure was a form of backlash to Kenya.
Duale said that though elections have dynamics, it was sad that the entire continent had thrown out "true pan-Africanism".
Regarding the East African Community, Duale noted that it was high time Kenya focused on its national interests and its citizens.
"This election has taught us huge lessons. We now know who are our true friends in East Africa and Africa at large. We are going tolook for friends who will put the interests of our people and our country first," he said.
-The Star