There are fears tiny pieces of plastic floating in the Indian Ocean could be affecting the reproductive health of manta rays and whale sharks.

The first ever international study to determine the impact marine microplastics are having in Western Australia, Indonesia and the Philippines will begin this summer.

Although there is considerable knowledge about plastic pollution, comparatively little is understood about what happens when they degrade into tiny pieces smaller than five millimetres in diameter.

Researcher Ellie Germanov has embarked on a PhD project through Murdoch University to determine whether filter-feeding animals were being harmed by the presence of microplastics off the coast of Bali, beaches in the Philippines, and Coral Bay reefs in Western Australia.

"Anything that is large at the moment and floating around is going to become smaller and smaller, and become microplastic size, which increases its likelihood of being ingested by animals," she said.

Ms Germanov said increasing levels of marine plastic debris were a global environmental problem, and the waters of South-East Asia were some of the worst affected areas on the planet.

"This is something that is affecting the entire marine environment and deserves attention from policymakers in terms of reducing the amount of plastics that are available," she said.

Approximately 3.2 million tonnes of mismanaged plastic waste is being disposed of in Indonesia annually, with up to 40 per cent entering the marine environment.

Over the next four years Ms Germanov will measure the levels of microplastics in the feeding grounds of manta rays and whale sharks in the three countries, as well as examining materials in the guts of the animals.

Ms Germanov said anytime an animal ate indigestible plastic, it had negative health implications.

"The plastic can block up the digestive tracts reducing the ability to absorb nutrients, which may ability to reproduce and have population wide effects," she said.

Ocean plastics pose long-term threat

Murdoch University researcher Ellie Germanov will measure the levels of microplastics in the feeding grounds of manta rays and whale sharks. ( ABC News: Laura Gartry )

While the WA coast appeared to have less rubbish floating around, researchers had found a microplastics hot spot just near the World Heritage-listed Ningaloo reef.

Strong currents may also sweep particles from as far away as South Africa.

Such rubbish is a serious threat to marine life and does not sink away quickly.

A plastic water bottle can take hundreds of years to degrade, while a plastic bag can take decades.

But the latest threat could be even more toxic and harder to prevent.

Some cosmetic products including toothpaste and facial scrubs contain tiny chemical plastic beads that are small enough to pass through filters, so millions ended up in the ocean.

"These small pieces are not filtered by our water treatment so they also end up in the water," Ms Germanov said.

"So despite waste management perhaps being better in Australia, there are still microplastics entering the water from other sources."

Biological samples taken in the study would be analysed at Murdoch University to establish if toxins such as pesticides and industrial chemicals were building up in the animals.

Ms Germanov's research is being conducted with the support of the Marine Megafauna Foundation.