"The biggest issue is New Zealand against the rest of the world," he said.
The country had significant competition in export markets "so we need to lower our total cost".
Ports of Auckland chief executive Tony Gibson said both council-owned ports were gateways to two of the largest North Island provincial economies "with significant growth and demands on infrastructure".
Supply chain scale and efficiencies would give greater resilience and help lower costs to exporters and importers.
"There is a natural fit between Ports of Auckland and Napier Port," he said.
"We share a similar way of working, common customers and supply chain opportunities and have similar ownership structures so that's a great base to work from."
Mr Cowie said the alliance could lead to staff exchanges to share best practice and innovate in technology, health and safety and sustainability.
"Napier Port's vision is to be central New Zealand's leading provider of port and logistics solutions. This alliance fits with the natural flow of freight in the North Island, based on ports close to demand centres and Auckland's weighting towards imports and our strong export base," he said. "Both operators are committed to growing our talent so we will be developing a joint talent pool, driving skills development and opportunities like staff exchanges where it makes sense.
"The alliance is a significant and exciting development for local exporters and the local community. Better international freight links will benefit the Hawke's Bay region, encouraging additional investment and supporting the growth of local employment opportunities."
ExportNZ Hawke's Bay executive officer Amanda Liddle said other businesses should consider similar collaboration. "It is a win-win situation for all exporters, as it will lead to an even more streamlined approach."
Napier Port had another record year of container volumes for the 2016 harvest season. Log volumes are forecast to increase from 1.1 million tonnes to 2.4 million tonnes by 2025.
A new wharf planned will be its biggest single investment since it was established in 1886.
Auckland is also growing and in June was named Best Seaport in Oceania at the Asian Freight, Logistics and Supply Chain Awards. Plans to increase its berthage have met strong opposition and a recent Port Future Study recommends a move to a new location in the long-term.
-Video hbtoday.co.nz