The third cyclone in a month is bearing down on Australia after it was initially predicted not to make landfall.

Tropical Cyclone Nathan has been swirling around in the Coral Sea off far north Queensland for the past nine days, but is now expected to hit in the rural region around Cooktown, north of Cairns.

The Australian Bureau of Meteorology issued a warning to communities in the area that the cyclone, currently a category three storm, would likely hit in the early hours of Friday local time.

The threatened areas are not heavily populated, and Nathan is unlikely to cause the widespread devastation caused by tropical Cyclone Pam in Vanuatu this week.

But a category five tropical Cyclone Nathan "cannot be ruled out", the Bureau of Meteorology said in its warning issued on Thursday.

Flash flooding from heavy downpours is expected.

Meanwhile regions in southern Queensland are experiencing record autumn high temperatures.