In the EU, maritime transport is responsible for 13.5 per cent of transport emissions, slightly behind aviation at 14.4 per cent and far behind road transport at 71 per cent.
Seventy-seven per cent of external trade and 35 per cent of trade among member states is transported by sea.
The EU's emissions from domestic navigation have decreased 26 per cent since 1990, but it still accounts for 16 million tonnes of CO2.
'Continued action to reduce its environmental footprint is needed for the sector to play its part in turning Europe into a climate-neutral continent by 2050,' said the report.
The report added that extra efforts are needed toward 'meeting our zero pollution ambition and halting and reversing biodiversity loss'.
However, as shipping activities are expected to grow over the next several years, so will their associated emissions.
In 2020, the UN agency controlling the environmental impact of international maritime transport (IMO) projected an increase of shipping emissions of 90 per cent and 130 per cent by 2050 compared to 2008.
Said European Environment Agency head Hans Bruyninckx: 'The maritime transport in Europe and the entire international shipping community has an urgent responsibility to step up their efforts to reduce this sector's environmental footprint.'
'Much more is needed for a fundamental shift towards a sustainable maritime transport sector that contributes to secure the future well-being and survival of our most sensitive ecosystems and coastal areas, and the well-being of Europeans,' said Mr Bruyninckx.