The Irish Exporters Association has said that a European directive on low-sulphur fuel will increase shipping costs by 40%.
The European Council, Commission and Parliament have signed an agreement to reduce sulphur content in marine fuels.
The measures take effect in the North Seas, Baltic and English Channel from January 2015 and in all other European waters from January 2020.
Friends of the Earth said that marine fuel was the dirtiest form of transport fuel.
The Exporters Association says reducing the level of sulphur in fuels and limited refining capacity will add to fuel costs.
John Whelan, CEO of the Irish Exporters Association said that their view is that freight costs for exports could increase by as much as 25%. He said that the association weren't opposed to cutting sulphur emissions but that the time frame, in their view is "completely unreasonable".
He called on the Government to immediately seek a derogation from the directive.
Friends of the Earth Director Oisín Coghlan said that the day of Ireland seeking directives has passed and come to an end.
He said that marine fuel is the dirtiest form of transport fuel. It's gone on land, he said, and now it is time to get rid of it at sea.
It's a heavy oil, he said that sinks to the ocean floor when in the sea and does untold damage to the marine ecology.
