The cash-strapped ports authority faces an internal revolt over plans to spend millions moving its two main offices, in Johannesburg and Durban, to the Port of Ngqura in the Eastern Cape.
The Transnet National Ports Authority (TNPA) has issued a relocation plan to 400 affected staff who have been instructed to report for work from April 1 at Ngqura, which handles just a fraction of the country's shipping cargo.
Trade unions say the plan was presented as a fait accompli - without the required staff consultation - and maritime experts have questioned the TNPA's motives.
Durban is Africa's biggest port and Johannesburg is one of sub-Saharan Africa's most important economic hubs. By comparison, Ngqura, 20km outside Port Elizabeth, has only welcomed commercial vessels since 2009.
The government has earmarked the Eastern Cape for maritime investment ranging from new bunkering services to shipbuilding.
However, a prominent Cape Town maritime personality, who did not want to be named, said Ngqura was at least a port, whereas the Johannesburg head office was 600km inland.
"While Durban, as the busiest port and with a significant TNPA presence already, might be the logical choice, Ngqura/Nelson Mandela Bay is almost central along the coast, though with modern communications that need not be a major consideration," he said.
One TNPA employee said staff suspected the move was linked to the appointment of new TNPA CEO Pepi Silinga, who previously led the Coega Development Corp (CDC). Ngqura forms part of the CDC.
In a Transnet staff memo sent in late December, the company said the relocation rationale aimed to create a national spread of head office locations, strengthen geographic ties to and with coastal regions, and encourage local economic development.
The Johannesburg (Parktown) and Durban (Kingsmead) offices would be consolidated inside the TNPA's new R255m eMendi building.
"Occupying our own buildings is part of our cost-containment strategy and the building is being recapacitated to accommodate us," the memo said.
But the renovation and relocation costs would require significant money at a time of economic strain, said United National Transport Union general secretary Steve Harris.
"If you look at the current state of the economy, where is the business plan behind this? To us as labour it just doesn't make business sense," Harris said. "What additional business will that move bring to an area like Port Elizabeth? It's not like they're bringing business down there. They are only going to occupy the offices."
The South African Transport and Allied Workers Union said it would make a statement after consulting members, but one of the union's leaders said Transnet still needed to explain the logic behind the move.
"We want to know the pros and cons. Right now it is just a proposal from the group chief executive. It has not yet been finalised," the official said.
Correspondence between staff representatives and TNPA chief people officer Khaya Ngema suggests the matter is concluded, prompted partly by the expiry of the company's office leases - in September last year in Parktown and in April in Durban.
"The company has taken a principled decision that its offices must be relocated to Transnet-owned properties," Ngema said. The Transnet buildings in Ngqura had long been underused and were "appropriate" for a new head office, he added.
"The process of getting the building ready and fit for purpose for TNPA is already under way, with various streams working on the project.
"Stopping the process at this stage would therefore be impractical."
In a letter to Ngema in December, Harris said the relocation decision breached an agreement to consult labour on crucial decisions.
The TNPA did not respond to Sunday Times queries.
