Chief executive Charles Hammond said Danish operator DFDS had told him the Rosyth-Zeebrugge route would close as hauliers will not pay higher charges forced by sulphur emission limits from January.
DFDS said it would switch from heavy fuel oil to low-sulphur marine gas oil to meet the new European directive. However, Forth Ports said this would increase charges on the freight-only ferry by 20 per cent, prompting firms to switch to English ports.
Hammond said: “Unless something changes, DFDS will move the ship to its Teesport route.”
In a letter to First Minister Alex Salmond, he said there was a “real and immediate risk of losing this service”. He said DFDS had indicated the extra cost of complying with the regulations “is unlikely to be borne by their customers and therefore the route will become unviable”.
Hammond has called on the Scottish Government to help cut Rosyth’s impending extra charges. However, it is not clear whether this would be permitted by competition laws. He also wants ministers to consider taking over the route, using another ferry which has “scrubbers” to limit emissions – too expensive to install on the current vessel.
DFDS spokesman Gert Jakobsen said: “We have made no secret of the fact the regulations present a huge challenge for us.”
A Scottish Government spokesman said: “The future of the route is a commercial issue for DFDS, although the Scottish Government recognises the challenges they face.
“We understand DFDS has been consulting customers on the options to deal with the impacts of the EU Sulphur Directive, which comes into effect next year.
“The Scottish Government has provided significant support to the service, within EU State Aid rules, and will continue to support any proposals for EU funding brought forward from the industry that could help mitigate the impact of the EU Sulphur Directive.”