South African diplomats also met with the US Embassy's Charge d'Affaires Monday to express their concerns.
In a statement, the South African Department of International Relations and Cooperation (DIRCO) didn't specifically mention the vulgarity but said it was concerned about "statements that were allegedly made by President Donald Trump" concerning African nations.
DIRCO noted South Africa's contributions to the United States and said international reactions "clearly serve as a united affirmation of the dignity of the people of Africa and the African diaspora." The statement also noted that Monday was Martin Luther King Day in the United States.
The US Embassy and its top diplomat responded by saying, "there has been no change in the United States' dedication to our partners across the Continent" and that "the United States deeply respects the people of Africa and ... South Africa," according to the DIRCO statement.
No US reaction to the meeting was immediately available.
During an Oval Office meeting on immigration Thursday, Trump expressed frustration with people coming to the United States from countries in Africa and elsewhere, sources told CNN.
Trump on Friday denied describing certain nations in such vulgar terms
, tweeting: "The language used by me at the DACA meeting was tough, but this was not the language used." He also defended himself Sunday night, telling reporters he is "not a racist."
Prior to the meeting at the US Embassy in Pretoria, the South African Department of International Relations issued a statement, saying "The Department will provide an opportunity to the Charges de Affaires to explain the statement that African countries, alongside Haiti and El Salvador, constitute 'shitholes' from where migrants into the United States are undesirable."
The statement said the government noted Trump's denial that this exact language was used but said it "has noted further that President Trump's denial was not categorical, referring only to Haiti and not addressing the entirety of the statement attributed to him."
"South Africa aligns itself with the statements issued by the African Union and the Africa group of Ambassadors to the United Nations in New York. Africa is united in its affirmation of the dignity of the people of Africa and the African diaspora."
US confirms diplomats summoned
Under Secretary of State Steve Goldstein told CNN that the top US diplomats in South Africa and Ghana had been summoned to meet with the governments on Monday.
The governments of Haiti, Botswana and Senegal also summoned US diplomats in those countries in the past few days. The State Department is expecting more diplomats to be called in this week, Goldstein said.
The "President has the right to make whatever remarks he wants and we respect the President," Goldstein said, but he noted that diplomats had been instructed to "reaffirm that the US remains committed to its relationships with these countries and cares deeply about their people."
"They will have to work extra hard to send that message right now, but that's part of their responsibility. It doesn't change what they do," Goldstein said.
State Department officials said diplomats have been advised not to try to interpret or soften the President's remarks but rather to listen and acknowledge the countries' concerns.
The envoys have been instructed to emphasize areas of shared cooperation, which transcend any comments that may have been made by the President, officials said.
'Infuriation, disappointment and outrage'
The African Union, a group representing the continent's countries, and African ambassadors to the United Nations Friday sharply denounced Trump's reference to African nations as "shitholes"
and called on him to retract his statement and apologize.
"The African Union Mission wishes to express its infuriation, disappointment and outrage over the unfortunate comment made by Mr. Donald Trump, President of the United States of America, which remarks dishonor the celebrated American creed and respect for diversity and human dignity," the African Union mission to the United States said in a blistering statement.
Condemning the comments "in the strongest terms," the AU demanded "a retraction of the comment as well as an apology, not only to the Africans, but to all people of African descent around the globe."
African UN envoys issued a statement saying their group is "extremely appalled at, and strongly condemns the outrageous, racist and xenophobic remarks attributed to the President of the United States of America."
The envoys released a joint statement Friday after an emergency meeting was held to address the issue.
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 color," it said.
'Sounds like fake news'
Other governments in Africa have also responded angrily.
The government of Botswana said it had summoned the US ambassador to the southern African nation to "express its displeasure" over Trump's reported comments, which it views as "highly irresponsible, reprehensible and racist."
The government said it had also asked the United States to "clarify if Botswana is regarded as a 'shithole' country."
"I am shocked by the words of President Trump on Haiti and Africa," Senegalese President Macky Sall said in an official tweet.
"I reject them and condemn vigorously. Africa and the black race deserve the respect and consideration of all."
A senior official from Somalia, also on the US list of TPS nations, told CNN that Trump's comments were unworthy of a response.
"It sounds like fake news to me," Somali Information Minister Abdirahman Omar Osman said by phone from Mogadishu. "If it's real, it doesn't need a response. Those comments do not deserve a response."
Newsmakers and ordinary citizens have also reacted on social media.
South Africa's best known morning-news anchor Leanne Manas tweeted Friday: "Good morning from the greatest most beautiful 'shithole country' in the world!!!"