Child pregnancies in Tandahimba have been on the rise.
In 2015 some 20 cases were reported while in 2017 some 27 cases were recorded.
Speaking during a district consultative committee meeting earlier last week, Mr Waryuba said the schoolchildren and their parents should be detained pending investigations.
His directive is part of the efforts to end pregnancies among students in the district.
Mr Waryuba said it was intolerable that 55 schoolgirls should be expelled from school because they are pregnant.
But gender and human rights activists have decried his directive. They argued that the authorities should arrest the men who sired the babies, not the students.