The UK maritime industry has also warned that tougher limits on sulphur emissions in the North Sea may even drive operators out of business.
A number of ferry companies said their fuel bills would rise by tens of millions of pounds a year, resulting in passenger fare increases of 20%, fewer services and job losses.
They also claimed that more traffic would be transferred to the roads and that higher freight costs would mean imported goods would cost more.
The so-called Annex VI controls, to come into force from 2015, are backed by the British government as part of an international convention revised in 2008.
The European Commission wants to bring the regulations into European Union law, but with additional requirements - resisted by the UK - for passenger ferries to observe the limits even when they are outside special emission control areas.
The Commons Transport Select Committee has supported the Government, saying the costs of tighter controls would be outweighed by the health benefits, estimated at £1.1 billion a year from 2020.
"Tighter emissions limits have been under discussion for many years, during which time shipping has enjoyed favourable treatment when compared with the emissions limits and fuel costs faced by the road haulage industry," the committee said in a report.
"However, we acknowledge that these regulations will impose significant costs on operators, and we therefore agree that the Commission should impose no additional burdens on operators at this time over and above the requirements of Annex VI."
Maritime UK vice chairman Lars Olsson told the committee: "It will affect our businesses in a radical way and it may lead to route closures and loss of jobs, investment and so forth."