Trump, who reportedly made the comment during a meeting with legislators Thursday on immigration reform, drew charges of racism.
"Why are we having all these people from shithole countries come here?" Trump said, people briefed on the meeting told The Washington Post.
The New York Times later reported the same comment, citing unnamed people with direct knowledge of the meeting.
"The language used by me at the DACA meeting was tough, but this was not the language used," Trump tweeted early Friday.
The reference was to the Deferred Action for Childhood Arrivals (DACA) program, which shields from deportation nearly 800,000 immigrants brought to the country illegally as children.
Thursday's meeting was to discuss a compromise under which DACA would be preserved but a visa lottery and a policy allowing legal immigrants to bring family members into the country would be ended.
"I want a merit based system of immigration and people who will help take our country to the next level," Trump said in another tweet.
"USA would be forced to take large numbers of people from high crime countries which are doing badly," Trump tweeted.
The Post and the Times said Trump's vulgar remark Thursday was in reference to African countries and Haiti. The Post included El Salvador on its list.
Trump suggested the United States should instead welcome immigrants from places like Norway, whose prime minister met with Trump on Wednesday.
United Nations rights office spokesman Rupert Colville said "there is no other word one can use but 'racist'" to describe Trump's remarks.
Democratic congressman Luis Gutierrez called Trump "a racist who does not share the values enshrined in our Constitution."
(This story has not been edited by NDTV staff and is auto-generated from a syndicated feed.)