Condor says it has' no choice' but to increase freight costs by nearly 19%, after absorbing rising prices for three years.
The ferry company has responded following days of criticism of its planned hike in charges for bringing goods into the islands.
Jersey's Economic Development Minister Deputy Kirsten Morel said it was 'hard to see the justification' for increases that are 'so significantly above RPI'.
Condor CEO, John Napton says it has absorbed increases for three years to minimise the impact on its own customers;
"...but latterly have been subjected to significantly above-inflation rises in some port costs and other fees, which in some cases are between 18% to 35%, along with minimum and living wage increases.
We are notifying logistics clients of an increase in charges, which is obviously regrettable but having kept our charges low for the past three years, the rising costs mean we now have no choice but to pass these on."
Ports of Jersey fees will increase by 11.1% from January, while some Guernsey Ports fees are jumping by as much as 150% as it tries to reduce its reliance on public funds.
Mr Napton says the company's finances were impacted during the pandemic.
Strict rules on isolation on arrival in both Guernsey and Jersey saw visitor numbers plummet, while Condor continued to supply essential food and medicines to both Bailiwicks.
The Government of Jersey has asked Condor to 'justify' the increases, while the Committee for Economic Development in Guernsey says it is working with the company to make sure any increases are 'essential, affordable and proportionate'.
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