Ports at Tauranga and Lyttelton will lose ship visits when CMA CGM, the world's third-largest container shipping line, withdraws the weekly Nemo service at the beginning of August.
CMA cited rising costs as the reason to end the recently established service, and would instead use other trans-Tasman lines to carry the cargo to Melbourne, Lyttelton Port chief executive Peter Davie said.
Lyttelton Port would include an assessment of the impact of losing the Nemo service in its annual result in August.
"However, this was a business decision taken by CMA CGM to streamline its own operations -- CMA CGM has reiterated that our service levels were excellent and we were performing extremely well under the contract," Mr Davie said.
In February, CMA announced plans to dump its Nemo service from Ports of Auckland and consolidate in the North Island at the Port of Tauranga.
Port of Tauranga said that in the short time the service had been calling, the volume of containers exchanged at the port had been far larger than originally predicted.
"We understand that CMA CGM expect to offer alternatives to current Nemo customers through the other services that they, and sister company ANL, currently hub through Tauranga and we do not expect any material impact on container throughput," Port of Tauranga said.
Port of Tauranga shares lost 2c to $6.83, and Lyttelton Port shares fell 5c to $2.20.