The European Parliament has approved the draft EU rules that demand ship owners using EU ports to monitor and report CO2 emissions each year.
The new rules will come into effect from 2018 for ships of more than 5,000gt, regardless of the country in which they are registered.
Portugal MEP José Inácio Faria said: "Maritime transport does not come under any greenhouse-gas emissions reduction measures"
"What we are looking at today is a first step to reduce emissions. If nothing is done, shipping emissions will go up by about 50% by 2030."
The new rules are aimed for an EU-wide system for monitoring, reporting and verification (MRV) of greenhouse gas emissions from shipping.
This process will help the EU enhance the information about ship efficiency and emissions and also encourage reduced emissions and fuel consumption.
It will also decrease the administrative burden on companies and make the measurements as accurate as possible.
José Inácio Faria added: "This legislation is applicable to all ships using European ports, and will be an opportunity to influence negotiations within the International Maritime Organisation (IMO).
"We need to make sure that cooperation with our international partners is kept, and make sure these steps give rise to an ambitious international agreement."
However, the rule will be not applicable to fishing vessels, warships, naval auxiliaries, wooden ships of a primitive build, ships not propelled by mechanical means, and government ships used for non-commercial purposes.