The Maritime Union of New Zealand is calling for national co-ordination of port strategy, arguing that Fonterra is exerting such power as a customer it is effectively rationalising the port industry.
General secretary Trevor Hanson is advocating a "KiwiPort" concept, where ports are integrated and nationally co-ordinated with a level of public ownership.
But there is no detail on the idea. Hanson says there is unlikely to be a return to the days when the port authority directed investment in ports in the current "capitalist" environment.
Hanson says since port reform in the late 1980s, successive governments have had a hands off approach to ports, which has led to an unstable industry.
This month Fonterra announced big changes in its export shipping , switching shipment of product made at its Clandeboye plant in South Canterbury from Timaru to the container terminal at Port Lyttelton for the next five years, and dropping the port at New Plymouth to ship production from its Whareroa plant near Hawera through Auckland, Tauranga and Napier.
The Timaru and Taranaki ports will each lose about a third of their cargo volumes in the changes, while Lyttelton will pick up a boost of as much as 10% in its container traffic.
Hanson says decisions by Fonterra and major shipping companies are harming regional communities and regional ports.
"There needs to be oversight and regulation so we have a planned port industry that has stability, rather than the massive waste of resources that goes into duplicating infrastructure and machinery for the sake of destructive competition, and the instability that it creates for skilled employment in New Zealand ports."
Port Taranaki spent $20 million to deepen the port for larger vessels.
"What we are seeing is the destructive rationalisation of New Zealand ports regardless of national interest, secure jobs, economic development and stable regional communities, to suit global shipping companies and the short term interests of a dairy conglomerate."
Fonterra has argued that the nation's freight sector should be focusing on building ocean cargo capacity, and flexibility in making connections to the shipping routes to key markets, rather than rivalry between individual ports.
The nation's international competitiveness depends on its ability to connect directly with the large consumption markets in the US and Europe through Asia, Fonterra's general manager of supply chain strategy, Nigel Jones, said earlier this month.
By railing product to Auckland, Tauranga and Napier, Fonterra could connect with up to a dozen shipping lines, Jones said.
Government-owned KiwiRail has declined to comment on what proportion of its business will be from Fonterra or on the profitability of that business. It has a large and increasing volume from the coal industry.