"This is a specific case of a certain number of African states taking the initiative to create a dedicated force to fight terrorism. So, we don't understand how the United States could hold back or not engage in the fight against terrorism," Faki said in an interview with AFP.
Faki's January election as chairperson of the AU commission came days after the inauguration of US President Donald Trump, who has proposed slashing US funding for aid projects and multilateral institutions like the UN.
But the US stopped the Security Council from formally backing the force and opposes funding it.
Washington has argued that UN authorisation was not necessary because the troops will be operating in the territories of Burkina Faso, Chad, Mali, Mauritania and Niger, the countries that make up the force.
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However the real issue is seen to be willingness to commit UN funds to the mission and the question of financing still hangs heavily over the so-called G5 force, which will be headquartered in Mali.
"We hope that the new administration will be in step with the current challenges of the world," Faki said. "In any case, it does not seem opportune for the United States to disengage itself. These are fundamental questions which determine my faith for peace and stability in the world."
Last month the US pushed through a USD 600-million cut in the UN's budget for peacekeeping operations that will force the drawdown of a long-running peacekeeping mission in Sudan's troubled Darfur region.