The South African Press Agency reports that they left their house on Monday morning with money to enrol at the school for the 2011 session.
SAPA quotes Warrant Officer Lunga Mahonga as saying that they were pupils at Mondeor High School until the end of last year, when they went for a trip to Australia. The pair arrived back in South Africa last week.
Staff at the high school did not see the brothers on Monday and could not confirm whether they received enrolment forms..
The school's Principal Vangelia Nicolaou, who confirmed that they were originally from Nigeria, told SAPA, "The brothers were very nice boys. We can't understand how something like this could have happened."
Chukwuemeka was last seen wearing blue jeans, a pair of blue canvas shoes and a hooded jacket while Chibyele was in a pair of black skinny jeans, a dark blue jacket and red striped shoes.