The Foreign Minister Geoffrey Onyeama "shed light on the veracity or otherwise of the substance of the remarks, stressing that if they were true, they were deeply hurtful, offensive and unacceptable", the ministry said in a statement.
Trump reportedly made the remarks at a private meeting with lawmakers on immigration on Thursday. A U.S. senator who attended the gathering said the president used "vile, vulgar" language, including repeatedly using the word "shithole" when speaking about African countries.
The Nigerian foreign ministry statement noted the "very warm and cordial relations that presently exist" between Nigeria and the U.S.
The United States, represented by Deputy Chief of Mission David J. Young as the ambassador was not in Nigeria, said there were contradictory accounts as to whether the remarks were made, the statement said.
In a separate statement, a U.S. embassy spokesman said Young "reiterated the excellent relations that exist between the United States and Nigeria and they discussed future cooperation between the two countries".
The U.S. president on Friday denied using such derogatory language. But he has been widely condemned in many African countries and by international rights organisations. African Union countries demanded an apology on Friday.