The Catholic Church and other institutions then raised these children.
"In the name of the federal government, I apologize to the metis from the period of Belgian colonization and to their families for the injustices and the suffering that they went through."
The Prime Minister's apology marks the first time Belgium is taking official responsibility for the harm it caused during its colonial rule in Central Africa.
His remarks come shortly after a preliminary report released by the United Nations Working Group of Experts on People of African Descent after experts visited the country in February.
It added: "There is clear evidence that racial discrimination is endemic in institutions in Belgium.
"The root causes of present-day human rights violations lie in the lack of recognition of the true scope of violence and injustice of colonization."
Belgium's reign in Central Africa lasted from the 1800s to 1960 where King Leopold II exploited rubber and other resources.