Trump criticised immigration to his country from El Salvador, Haiti and the African continent, by calling the group "shithole countries" at a meeting with Congress members at the White House on Thursday, according to US media.
"The African Union mission to the UN is extremely appalled at, and strongly condemns the outrageous, racist and xenophobic remarks attributed to the US president as widely reported by the media," Martha Ama Akyaa Pobee, Ghana's ambassador to the UN, said on Friday.
The group has demanded a retraction and apology from Trump.
According to US media reports, citing people with knowledge of the conversation, Trump asked during a conversation about immigration: "Why are we having all these people from shithole countries come here?"
Trump suggested the US should instead focus its immigrant entry policy on countries such as Norway.
Following an emergency session of the African diplomats, Pobee added that the group "is concerned at the continuing and growing trend from the US administration towards Africa and people of African descent to denigrate the continent and people of colour".
The ambassadors' reaction comes after the 55-nation African Union said it was "frankly alarmed".
"Given the historical reality of how many Africans arrived in the United States as slaves, this statement flies in the face of all accepted behaviour and practice," AU spokeswoman Ebba Kalondo said on Friday.