Taranaki and Timaru ports will lose a big portion of their business because of a shake up by Fonterra.
The dairy cooperative has announced it will focus on exporting through the ports of Auckland, Tauranga, Lyttleton and Napier and will make better use of KiwiRail.
The changes are needed to reduce costs, get better returns for farmers and improve services to its global customers, the company says.
Fonterra's supply chain strategy general manager Nigel Jones says Fonterra has had to look for greater flexibility in its shipping arrangements following a major reduction in capacity provided by the shipping lines out of New Zealand.
That means channelling more freight through the most frequently-serviced ports and relying less on ports with indirect or feeder services.
The volume of product leaving from Taranaki will be reduced by 65% and by 80% from Timaru.
Both port companies say that equates to at least one-third of their export container business, but it's too early to speculate about possible job losses.
PrimePort Timaru chief executive Jeremy Boys says he had expected the move to be carried out over months or years, so was surprised that it had been brought forward so quickly.
Port of Taranaki chief executive Roy Weaver says Fonterra supplies about 60% of its container business and the proposed cutback will reduce container movements through New Plymouth from 65,000 to about 40,000.
However, the port will gain trans-Tasman cargo from Fonterra's Eltham plant, he says.
New Plymouth Mayor Peter Tennent says Port Taranaki has made a large investment to deepen the port, and exporters - including Fonterra - have reported significant competitive advantage from using it.
The Rail and Maritime Transport Union says a national port strategy is needed to prevent ports from spending millions of dollars attracting what can turn out to be short-term business.