Scientists say ex-Tropical Cyclone Oswald has killed thousands of turtle eggs and hatchlings at one of Queensland's biggest rookeries.

The Queensland Department of Environment and Heritage says galeforce winds and high tides have destroyed turtle nests at Mon Repos near Bundaberg.

An estimated 46,000 eggs have been destroyed.

Chief scientist Col Limpus says the weather came at the worst time for the young turtles.

"Galeforce winds coming in on very high tides and so it's eroded the nesting habitat for the turtles," he said.

"We had the maximum number of clutches for the year because not that many had hatched and the end result we lost about 60 per cent of all of the clutches that were in the beach."