The microscopic pellets, called nurdles, are the building blocks for most of the world's plastic production, from car bumpers to salad bowls.
The legislation from the European Commission, the EU's executive arm, had been expected but since there had been no information about when it would be published, NGOs and EU lawmakers feared the plans had been put on ice.
"Microplastics are pervasive and we need to stop the pollution at the source," the EU's environment commissioner Virginijus Sinkevicius said.
"Today's proposal aims to prevent the spill of plastic pellets in our environment, for the sake of our ecosystems and health, and in support of economic sectors that depend on healthy soils and clean, plastic-free rivers and oceans," he added.
The Rethink Plastic alliance of European NGOs cautiously welcomed the proposal, but called on the commission to look at other major sources of microplastics pollution.
"The European executive's strategy signals curtailed ambition in addressing all responsible sources of microplastic pollution with swift and binding measures," said Frederique Mongodin, of the Seas At Risk organisation.
The proposal demands operators handling pellets in the European Union take the necessary measures to limit the release of the material through mishandling.
The commission said that between 52 and 184,000 tonnes of pellets are released in the environment each year due to mishandling throughout the entire supply chain.
Companies will have to conduct risk assessments to ensure their operations are taking the right measures to avoid spillage. If there is spillage, they will have to act quickly to contain leaks and undertake cleaning operations if necessary.
The commission hopes the proposal will reduce pellet release by up to 74 percent.
Larger companies must have their plans verified by an independent operator and they risk sanctions for violations.
The proposal will become law after EU lawmakers and the 27 member states agree on a final version but that is unlikely to take place before European elections in June.
The EU has banned the sale of consumer products that have microplastics intentionally added, such as loose glitter as well as some cosmetics that contain microbeads.
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