The estimated R250-billion plan is aimed at meeting the rapid need for shipping container capacity at Durban port, which services most of the country.
The development and expansion of the ports are of national importance and a key pillar of the presidential infrastructure co-ordinating commission's strategic infrastructure project two and also part of the National Planning Commission's national development plan, which looks forward to 2030.
Durban's port can accommodate 2.9-million containers, but its expansion and a new excavated port would increase its capacity to more than 20-million.
Transnet is predicting that, at an 8% annual growth rate in containers coming through the port, the existing infrastructure will reach its limit in 2019, seven years from now, and a lack of container capacity will hamper economic growth.
So the need for more infrastructure is clear. As one city official said: "A new port is not a nice-to-have."
Durban's port needs to expand for the good of the city and the good of the country, but the big question is how the city will implement the plan and treat its residents.
Environmentalists and community leaders have already raised concerns about how the city is approaching residents.
They are also concerned about port creep, and the arrival of crime, smuggling, prostitution, trucks, pollution and logistics companies in their neighbourhoods, things that Clairwood, one of the affected suburbs, is already familiar with.
"We are not against development. We are against being bulldozed," says Desmond D'sa, chairperson of South Durban Community Environmental Alliance, a coalition of 14 environmental, community and church groups, which came together in 1995.
But if the government gets its way, Durban will be changing fundamentally for the next 40 years.
Suburbs that would be affected, directly or indirectly and based on the city's and Transnet's plans, include Athlone Park, Isipingo Beach, Merewent, Austerville, Merebank, Treasure Beach, Wentworth, Jacobs, the Bluff, Umbilo and Clairwood.
According to a document prepared by Transnet and the eThekwini municipality, titled 2050 Vision for the Durban-Gauteng Freight Corridor, "there is already pressure on the port, the roads and in back-of-port areas.
"Unless significant expansion takes place, South African economic growth will be constrained, and freight will be forced to relocate to more distant ports."
A small number of containers are moved in and out of the eThekwini municipality, according to the city's Back of Port: Concept, Framework, Precinct Plans and Zoning Framework report.
"[But] the vast majority of containers remain in the municipality, where they are packed, unpacked and stored in empty container depots."
The report states that logistics companies that unpack the containers are unlikely to be more than 40km from the Durban container terminal, but most will be within 15km.
"Areas that 50 years ago were considered sufficiently peripheral to ports to warrant non-port-related activities, such as manufacturing, and are now within a 10km radius of the port are subject to market-related pressures to accommodate facilities that perform a logistics function," the report states.
Herein lies the rub: some of these areas are not just for manufacturing and include residents in suburbs such as Clairwood, which has already been invaded by illegal trucking and logistics businesses.
The 2050 vision envisions a three-pronged strategy, the first being short-term developments within the existing port to increase capacity, which will take place between 2010 and 2020.
The second phase includes the excavation of the dug-out port at Reunion next to the old Durban airport, which will take place between 2020 and 2040. Digging is expected to begin in 2016 or 2017, but the project has not been given the stamp of approval yet.
The third phase includes the development of a new excavated basin at the Bayhead rail yards.
But the expansion and development of the ports is not limited to those sites.
Transport infrastructure must also be increased and the state plans to increase rail freight capacity from 25% of current freight to 73%, and reduce road freight from 75% to 27%, by 2041.
But this "reduction" in road freight is relative and will not reduce the number of trucks on the road – that is expected to increase by 123% over the next 30 years, while rail freight is expected to grow by 220%.
All of this is aimed at bringing down South Africa's shipping logistics costs, which are currently at an average of 15.9%. India's average is 6.7%, and the United States's is 7.7%.