Cyclone shelters have been opened for people in Borroloola and Numbulwar as Tropical Cyclone Owen strengthens and has the potential to reach a Category 3 system by early Thursday morning.

Key points: Tropical Cyclone Owen may reach category three

Tropical Cyclone Owen may reach category three A warning is in place for communities from Burketown in Queensland to Cape Shield in the Northern Territory, including Groote Eylandt

A warning is in place for communities from Burketown in Queensland to Cape Shield in the Northern Territory, including Groote Eylandt Gusts may reach 110 kilometres per hour in these areas

A warning is in place for communities from Alyangula in the Northern Territory to Burketown in Queensland, while a warning has been cancelled between Cape Shield and Alyangula, and a watch remains in place east of the Queensland border for other Gulf communities.

Gales with gusts up to 110 kilometres per hour may develop between Alyangula and the NT/Qld border, including Groote Eylandt this evening, and destructive winds with gusts of up to 130 kilometres per hour may develop in coastal areas near Borroloola tomorrow.

Schools in Borroloola and Numbulwar will not open as they are being used as public shelters.

Residents between Port Roper and Alyangula on Groote Eylandt are being urged to take shelter as worsening conditions affect the region in the next six to 12 hours, while those in the Bing Bong and King Ash Bay residential areas are being evacuated to Borroloola.

"We've been in regular contact with communities around the Gulf of Carpentaria to make sure they've finalised their preparations," Regional Controller Travis Wurst said.

"This includes making sure their cyclone kits are well stocked, and they know where to take shelter if they don't think their home is strong enough to withstand gale force or destructive winds."

The system is forecast to change course on Thursday, moving eastwards towards the Queensland coast.

It may reach Category 3 intensity by Thursday morning, according to the Bureau of Meteorology, and a coastal crossing along the southeast Gulf of Carpentaria between Burketown to Pormpuraw during Friday afternoon is most likely.

Mr Wurst said extensive planning and preparation has been undertaken locally in the areas impacted by the warning, as well as at a regional level.

"Local community meetings have been held across the north-east Top End," he said.

"Communities are well aware of the cyclone warnings and are making preparations."

Heavy rainfall is also expected to develop about the islands and coastal areas of the western and southern Gulf of Carpentaria, with a marine wind warning issued for the Roper Groote Coast.

Boaties rescued as authorities warn against travel

Northern Territory Police are in the process of trying to rescue three fishermen in distress on a boat near South West Island in the Gulf of Carpentaria.

The boat is in an area where Cyclone Owen is bringing strong winds, particularly on the water.

An EPIRB has been activated and police say they believe the fishermen suffered a mechanical failure.

"Anyone thinking about venturing out to sea over the next several days is urged to reconsider their need to travel while these dangerous weather conditions are impacting the area," Mr Wurst said.

The forecast track map for Tropical Cyclone Owen, issued on Wednesday afternoon ( Supplied: BOM )

"We're asking people in the area to be prepared for these wet and windy conditions.

"Make sure your homes and emergency kits are prepared and your friends and neighbours are aware that this system is coming."

The Bureau of Meteorology has not yet issued a flood warning for the area and at this stage there is a low chance of storm surges.

But Mr Wurst said people travelling through the area should still take care and stay away from flooded roads and waterways.

"You don't know what the road conditions are," he said.

"There could be submerged branches or trees, and crocodiles are an ever present danger in the Top End."

A list of what residents should include in their emergency kit can be found on the Northern Territory Emergency Service website.

Cyclone preparedness information is available at SecureNT, and more information on weather warnings is available on the BOM website.