The carrier had already spilled about 50,000 tons of coal into the sea after it split in two when it ran aground last month, the South African Government News Wire reported Monday.
Officials said the wreck was not blocking shipping lanes at the Indian Ocean port.
The South African Maritime Safety Authority and the salvage team working on the vessel filed an emergency request to dump more coal as its only option.
The Department of Environmental Affairs gave approval after consultations with municipal, wildlife, agriculture and other officials, the report said.
"Although there are important estuaries, such as the uMfolozi, uMlalazi and the uMlathuze Sanctuary near the area where the vessel ran aground, the area directly around the vessel is not a biological diversity hot spot," the Department of Environmental Affairs said.
"It is, however, an industrial area, which is dredged annually. Nonetheless, the department will do all it takes to ensure that these neighboring estuaries are not affected by the salvage operation."