Tropical Cyclone Owen is forecast to strengthen over the southern Gulf of Carpentaria before moving eastwards towards the Queensland coast.
The latest warning from the BoM issued at 5.21am Wednesday says the warning area stretches from Cape Shield in the Northern Territory, to Burketown in Queensland, including Groote Eylandt and Mornington Island.
Tropical Cyclone Owen which officially re-formed as a cyclone yesterday is now a Category 1, with sustained winds near the centre of 75kph with wind gusts to 100kph.
The cyclone is currently 170 km east southeast of Groote Eylandt and 220 km northeast of Borroloola and is moving west at 12kph.
Tropical Cyclone Owen is located northwest of Mornington Island – with evacuations in place on the island – and is expected to move west today and then change course to move east back towards the Queensland coast on Thursday.
It may reach category 3 intensity by Thursday if conditions remain favourable.
The BoM said a coastal crossing along the southeast Gulf of Carpentaria coast during Friday was most likely.
Gales with gusts up to 110kph may develop between Cape Shield and the NT/Queensland border on Wednesday.
On Thursday gales may extend to Burketown, including Mornington Island, if the system follows a more southerly track.
Destructive winds with gusts to 130kph may develop in coastal parts near Borroloola and to the border early Thursday if the system takes a more southerly track.
Heavy rainfall is likely to develop about the islands and coastal areas of the western and southern Gulf of Carpentaria on Wednesday and Thursday.
Public shelters are now open.
The BoM said if not sheltering at home, go immediately to shelter with family, friends or at one of the public shelters and take your emergency kit with you
Make final preparations to home shelter and take shelter as gales arrive and businesses should shut now and send staff home or into shelter.
It is unlikely to affect the Mount Isa region though storms and showers are predicted to Friday.
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