The North East Corridor, which mostly moves chrome, ferrochrome, phosphate and magnetite, links South Africa to Eswatini, Zimbabwe, Mozambique, Zambia and the Democratic Republic of Congo.
Transnet said partial service had been restored after "an extensive safety exercise" by its engineers.
Operations commenced "in earnest" on Monday across the network, Transnet said in a statement, with teams "now working on clearing staged trains and the backlog on the Witbank to Richards Bay corridor, a channel for export(ing) coal, chrome and ferrochrome".
Work was still underway to restore service on the remaining part of the network
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