Reform of the EU's banana import regime cost Fyffes €41m in 2006, the company said in its full-year results.
Most of the cost came down to the higher tariff of €157 per tonne payable on imports of bananas since 1 January 2006.
The group also blamed costs of €7.3m on the demerger of its general produce and distribution business, now called Total Produce, and the demerger of its property assets to Blackrock.
Turnover in the produce and distribution business rose 13.9% to €1.99bn, while operating profit for the division inched up to €38.9m.
Chairman David McCann said: "Fyffes also experienced significant cost inflation in 2006, with fruit, shipping and fuel all more expensive, combined with less favourable average exchange rates and lower average banana selling prices on the Continent."
Fyffes' winter melon joint venture in Brazil, acquired towards the end of its 2005/06 season, was loss-making in the first year.