The commission's inquiries showed that the cost of sending a 20-foot container from Auckland to export ports such as Singapore, Long Beach and Shanghai was "considerably more expensive" than sending one from Sydney.
This was likely to reflect the lower freight volumes moving out of New Zealand, which meant the fixed costs for ships had to be spread across fewer containers, the report said.
The commission's report found that the nation's port and border charges compared favourably with other OECD nations including Australian but the performance of port companies varied across the country and showed room for improvement in workplace productivity and governance.
The commission singled out Port of Tauranga as having an approach that "works well for its owners and customers, where majority owner Bay of Plenty Regional Council treats the port as a financial asset to be managed on commercial terms and with contestable containerised freight handling.
Other ports "are leaving money on the table" via a lower level of workplace productivity. It recommends a more commercial focus for council-controlled ports and the exclusion of elected officials and council staff from board membership.
It cited submissions from the NZ Shippers' Council that Ports of Auckland has a diminished appetite to demand significant efficiency and productivity gains since the city took 100 per cent ownership of the port and it was delisted from the NZX.
For unions, it recommends reforms to the Incorporated Societies Act "to ensure modern governance structures and practices."
Finance Minister Bill English said the government "will look at the Productivity Commission's recommendations and carefully consider its response over the coming months."