He has been backed by two Republicans who were at the White House meeting, but Democratic Senator Dick Durbin said Mr Trump called African countries "shitholes" several times and used "racist" language.
South Africa's foreign ministry called the remarks, which sources said Trump made earlier this week during a meeting on immigration legislation, "crude and offensive" and said Trump's subsequent denial was not categorical.
Describing the comments as "extremely unfortunate", President Nana Addo categorically stated that Ghana is "certainly not a racist country".
Botswana's government on Friday condemned Trump's reported disparaging remarks about developing countries, calling on the Southern African Development Community (SADC), the African Union and all other progressive nations across the world to strongly condemn the remarks. "We will not accept such insults, even from a leader of a friendly country, no matter how powerful", the President said in a tweet.
Akinwumi A. Adesina - the President of African Development Bank came out emotional to comment on President Trump's statement. I congratulate Botswana for showing the way.
But in another tweet on Friday the president denied that he insulted Haitians.
Botswana summoned the U.S. ambassador to the country to "clarify if Botswana is regarded as a "s***hole" country", according to a foreign ministry statement calling Mr Trump's comments "irresponsible, reprehensible and racist".
"By declaring 2018 the African Anti-Corruption Year, the African Union (AU) policy making organs have given a strong push forward in our collective efforts towards a peaceful and secure Africa..."
The Mission also demanded a retraction of the statement and an apology from the U.S. President.
Ebba Kalondo, spokeswoman for AU Chairperson Moussa Faki, told AFP that Trump's statement "truly flies in the face of accepted behaviour and practice".
It said the "remarks dishonour the celebrated American creed and respect for diversity and human dignity".
"While expressing our shock, dismay and outrage, the African Union strongly believes that there is a huge misunderstanding of the African continent and its people by the current Administration", the AU added.