The chair of the group Moussa Faki said he had received a letter from Mr Trump and said Secretary of State Rex Tillerson’s current five-country “listening tour” on the continent reaffirmed the US commitment.
The pair met in Addis Ababa, Ethiopia and discussed a number of issues including trade, counter-terrorism efforts, Chinese investment, and development.
Just last month Mr Faki had written in a statement that the AU "condemns the comments in the strongest terms and demands a retraction of the comment as well as an apology to not only the Africans but to all people of African descent around the globe”.
Mr Trump has denied making the remarks - attributed to the President by Democratic Senator Dick Durbin - during a meeting about immigration, during which he also reportedly wondered why the US did not have more immigrants from places like Norway, whose Prime Minister he had just hosted.
Press Secretary Sarah Huckabee Sanders had said in response that “the President hasn't said he didn't use strong language, and this is an important issue, he's passionate about it, he's not going to apologise for trying to fix our immigration system."
"At this stage, nothing has changed with respect to our relationship with African nations and we continue to see them wanting to strengthen our relationship," Mr Tillerson told Buzzfeed News in the wake of the reports about the comment.
The President’s alleged sentiment is not the only point of contention between the parties, however.
Last month, as part of the apparent attempt at damage control, Mr Tillerson also claimed that during the last “successful” meeting with the AU “one of their greatest concerns is counterterrorism”.
However, the Trump administration slighted one of its most robust African counter-terrorism partnerships by placing a travel ban on people from Chad, Mr Faki's home country.
Chad assists in the fight against Isis-West Africa, al-Qaeda, and Boko Haram.
Mr Faki and Mr Tillerson also discussed Chinese investment in the African Union, an issue Africa Command’s Marine General Thomas Waldhauser told the House he was concerned about in Djibouti.
It also hosts a Chinese military base and recently seized control of the port from a private company to reportedly turn it over to the Chinese.
Ethiopia is another example of growing Chinese influence. The US has invested $567 million, while Chinese investments amount to about $15 billion.
They have also constructed shopping malls, stadiums, and host nation government buildings, prompting Mr Waldhauser to say at the House Armed Services Committee meeting that the US will “never outspend” China on the continent.
Mr Tillerson has said in the past that though that he thought China’s investments on the continent “encouraged dependency” versus the forms of US aid, which promotes “sustainable growth” - a perspective with which some global development experts have disagreed.
He was referring to some of the African nations who have defaulted on loans from Chinese companies and those that still lack jobs for domestic populations despite the Chinese projects going on in the country.
"We are not in any way attempting to keep Chinese investment dollars out of Africa. They are badly needed. However, we think it's important that African countries carefully consider the terms of those investments,” Mr Tillerson said in Addis Ababa.
Mr Faki was quick to point out though that Africans are "mature enough" to handle who invests in their countries on their own. He noted there was no one country that controlled the ability of others to invest in the continent either.
Mr Tillerson’s trip will also include visits to Djibouti, Kenya, Chad and Nigeria.