"Transnet's internal audit contract is arguably the biggest outsource contract of its nature in the world," Transnet spokesman Mboniso Sigonyela said in a statement.
Sekela Xabiso was one of three companies chosen by the Transnet Board of Directors' Audit Committee.
Nkonki Inc, another local South African firm, and KPMG were also picked.
During the first year the three will have a percentage of the work.
Sekela Xabiso would get 40 percent, Nkonki Inc 20 percent and KPMG 40 percent.
By the fifth year, Nkonki's share will rise to 35 percent, while Sekela Xabiso's share will peak at 45 percent.
The award follows last year's appointment of SizweNtsalubaGobodo, another black-owned accounting firm, as Transnet's external auditors.
Mafika Mkwanazi, Chairman of Transnet's Board of Directors said appointing such firms affirmed Transnet's commitment to broad-based empowerment.
"The two appointments are just two of the examples by which we at Transnet, as a state-owned entity, are providing the blueprint for meaningful and broad-based empowerment and skills development targeting black people, especially black women."
Transnet is rolling out a massive R300 billion rolling seven-year infrastructure investment programme to revamp and expand its port, rail and pipelines infrastructure.
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