Scientists found the eggs inundated for one or three hours showed no significant level of mortality.
However those underwater for six hours resulted in a 40 per cent increase in embryo deaths.
Dr Pike said this meant volunteers may be needed to physically move nests further inshore to save the species.
"We might be able to save them with people power," he said.
Raine Island, on the northern tip of the Great Barrier Reef, supports the world's largest green sea turtle nesting area, with as many as 60,000 females swimming from their feeding grounds thousands of kilometres away to lay their eggs.
But the turtle sanctuary is in danger of collapse due to rising sea levels and changes in the island's landscape.
Dr Pike said while inundation impacted the species' survival, the larger mystery surrounding the decline of green sea turtles on the island was yet to be solved.
He said turtle numbers were also likely impacted by other factors, including high microbial levels and heavy metals in the soil.
- AAP