Trump earlier announced that he had declared Nigeria a “Country of Particular Concern” because of the “existential threat” posed to its Christian population. He said “thousands” had been killed, without providing any evidence.
This is a designation used by the US State Department that provides for sanctions against countries “engaged in severe violations of religious freedom”.
Following this announcement, Tinubu said his government was committed to working with the US and the international community to protect communities of all faiths.
“The characterisation of Nigeria as religiously intolerant does not reflect our national reality,” the Nigerian leader said in a statement.
Jihadist groups such as Boko Haram and Islamic State West Africa Province have wrought havoc in north-eastern Nigeria for more than a decade, killing thousands of people – however most of these have been Muslims, according to Acled, a group which analyses political violence around the world.
In central Nigeria, there are also frequent clashes between mostly Muslim herders and farming groups, who are often Christian, over access to water and pasture.
Deadly cycles of tit-for-tat attacks have also seen thousands killed, but atrocities have been committed on both sides and human rights group say there is no evidence that Christians have been disproportionately targeted.
Trump has frequently expressed satisfaction over not having embroiled the US in a war during his tenure, and has cast himself as a peace-making president.
But the Republican leader is facing a growing number of voices domestically, particularly from the political right, who have drawn attention to the situation in Nigeria.
Additional reporting by Chris Ewokor in Abuja