New Zealand ship owners say they pay too much for greenhouse gas emissions when their rivals do not pay anything.
Their umbrella body, the New Zealand Shipping Federation, estimates the costs to be $250,000 in carbon charges per ship per year.
The fee is the result of the Emissions Trading Scheme, under which credits bought by fuel companies are passed on to customers, such as shipping operators.
The New Zealand Shipping Federation represents companies delivering oil from Marsden Point and running the Cook Strait ferries, as well as coastal traders like Pacifica.
Some of these services must compete with giant container ships that visit two New Zealand ports before returning to their home country.
They carry local cargo on the New Zealand leg of the journey, but do not pay emissions costs, unlike local companies.
Federation executive director Annabel Young said putting emissions charges on New Zealand ships was peculiar to this country, and was unwise because shipping was an environmentally sound means of transport.
"In other countries, and internationally, it is accepted the shipping is the most efficient way to move goods or people and, therefore, you don't want to penalise them by imposing carbon charges.
"It is a direct imposition on our costs and, at some point, it is going to feed through into the cost of moving freight and people by ships.
"It will have a disincentive effect."
Aviation industry moves to freeze emissions
The cost of credits on the New Zealand carbon market more than doubled in the past four years, putting an extra burden on shipping companies.
Shipping and aviation largely escaped controls under the Paris Agreement on climate change because they are international and so cannot be easily captured by individual countries' pledges.
Aviation aims to freeze emissions from 2021, despite not being covered by the Paris agreement.
Last October, the International Maritime Organisation unveiled a three-step plan to see whether further measures were needed for world-wide shipping.
The Organisation said it had already increased its energy efficiency with mandatory measures that came into force in 2013.