The Belgian government has apologised for the country's role in kidnapping thousands of mixed-race babies from their African mothers during colonial times.

Thousands of children in what are now the Democratic Republic of Congo, Rwanda and Burundi were taken away and raised in Belgian institutions.

Prime Minister Charles Michel said in a statement on Thursday that "on behalf of the federal government, I present our apologies to the mixed-race children born from Belgian colonisation and their families for the injustice and suffering they were subjected to".

He expressed "compassion for the African mothers, whose children were torn away from them," and concern for the emotional stresses the children went through.

Michel said he hoped the government recognition would be a step toward a collective national reckoning of Belgium's colonial past and in fighting racism today.