The Taiwanese vessel was seized in the harbour at Cape Town by inspectors from South Africa's Department of Environmental Affairs, after a spot-check revealed the undeclared haul.
It is reported that the vessel's skipper and 26 crew face criminal proceedings for providing false details of their catch. Under the country's Marine Living Resources Act, they could be fined up to R2 million and/or jailed for up to five years.
A spokeswoman for Marine and Coastal Management said that the crew had reported a take of nearly three tonnes of tuna, 1.36 tonnes of shark trunks, and 100kg of shark fins - far less than the weight of fins found in the boat's holds.
The crew's 100kg claim would have met the requirements of the South African permit under which the vessel entered the country's territorial waters and tied up in Cape Town.
The permit's rules reflect an international agreement that shark fins should not exceed five per cent of the weight of trunks brought back to port. The agreement was formulated in order to combat wanton finning and dumping of trunks - sometimes when the shark is still alive and facing certain death.
With between one-and-half and two tonnes of fins on board, under the agreement the Taiwanese fishing boat would have had to be carrying between 30 and 40 tonnes of shark trunks, way in excess of its actual cargo.