The birds - which as their name suggests, survive on a diet of bees - are found in the Northern Territory and Queensland, and roost in large numbers at the same sight each night between March and November.

The birds expel indigestible materials, such as bee wings, in pellets which are collected for analysis in a laboratory to help identify if the feral bee species, Asian honey bees, are active in the area.

Asian honey bees present a serious threat to native bees because they are major competitors for important resources such as nectar and pollen.

The effort is one tool in the armoury of the latest National Bee Pest Surveillance Program, which is led by Plant Health Australia.

Plant Health Australia surveillance national manager Sharyn Taylor said teams in Queensland and the Northern Territory would inspect thousands of pellets from Rainbow Bee-eaters over the next three years as part of the newly funded project.

"Rainbow Bee-eaters are common to much of Australia and well known to beekeepers as a bee predator," Dr Taylor said.

"However, ironically, they also play a vital role in protecting our local native bee populations, and they are excellent at finding bee populations, including exotic species."

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Surveillance officers have also deployed several automated catch boxes in remote locations that send an alert back to officers around Australia, whenever bees have entered the boxes, which detect new swarms of bees that arrive at ports from incoming vessels.

Hives of sentinel bees remain the backbone of the surveillance program, which is funded by Hort Innovation, Australian Honey Bee Industry Council and Grains Producers Australia.

The hives are placed at the ports of highest risk across Australia and inspected regularly for Varroa mite, the most important target for surveillance.

Australia is the only significant honey producing country that does not have the mite, which is responsible for devastating waves of colony collapses across the world.

Hort Innovation research and development manager Ashley Zamek said it was no coincidence Australia was free from many of the pests and diseases that pose serious threats to honey bees, and in turn the plant industries that are dependent on pollination.

"Australia's largely healthy honey bee population is the result of intensive, world-leading surveillance efforts combined with the vigilance and support of organisations and government agencies across the country," Ms Zamek said.

"This latest iteration of the bee pest surveillance program continues an initiative that is highly successful because of the deep collaboration involved."