The bodies want the UN International Maritime Organisation (IMO), which governs shipping, to push the industry to switch from sulphur-rich to cleaner-burning marine fuels. They say the move will cut the worldwide death toll by half and save the world up to US$275 billion a year.
"The IMO cannot continue to ignore mounting evidence that action to reduce air pollution from ships could avoid tens of thousands of premature deaths each year," said David Marshall, senior counsel at the Boston-based Clean Air Task Force, one of the groups calling for IMO to act quickly.
Scientists say that the fact that shipping takes place on the high seas -- away from populations who can readily see impacts of emissions -- was part of the reason its fuel standards lagged those of other industries.
Joao Viera, policy officer with the Brussels-based European Federation for Transport and the Environment said: "It is a disgrace that thousands are dying needlessly as a result of the IMO's intransigence on air pollution."
Viera warned the UN agency that if it failed to come up with an action plan in the next few months, the EU and other regional legislators would do the job for them.
The IMO could not immediately be reached for comment.
Friends of the Earth International has dispatched new scientific evidence to IMO policy makers showing a switch from high to low sulphur marine fuels can reduce premature deaths by 50 to 60 percent, or up to 50,000 lives per year.
The research, which links global emissions to heart and lung-related deaths, estimates mortality changes with falling sulphur content in marine fuels.
The pressure groups, which will be observing the IMO air pollution negotiations this week, want the shipping industry to slash nitrous oxide emissions by 90 percent and sulphur dioxide by between 70 to 90 percent, by no later than 2015.
International negotiations on new air pollution standards for ocean-going ships are at a critical stage at the IMO.
New tighter air pollution limits are expected to be adopted by countries party to the UN IMO later this year.
(Reporting by Stefano Ambrogi; editing by James Jukwey)