Severe Tropical Cyclone Owen is tracking slowly along the Northern Territory's north-east coast, and is expected to batter a number of tiny communities and islands as it moves east towards Queensland.

Key points: Three boaties have been rescued from the Gulf of Carpentaria

Three boaties have been rescued from the Gulf of Carpentaria Tropical Cyclone Owen is expected to turn back towards Queensland today

Tropical Cyclone Owen is expected to turn back towards Queensland today Schools in Borroloola and Numbulwar in the Northern Territory will not open today

Port McArthur, Bing Bong and a number of islands in the area are expected to be hit with sustained winds of up to 120 kilometres per hour this afternoon as the cyclone continues its path as a category three system.

A warning remains in place for Numbulwar in the Northern Territory, to Aurukun in Queensland, including Borroloola, Mornington Island, Karumba, Kowanyama and Pormpuraaw.

A watch zone now extends inland from Karumba to Aurukun as far as Georgetown, Chillagoe and Coen.

A warning from Alyangula to Numbulwar in the Northern Territory, including Groote Eylandt, was cancelled.

The storm is expected to intensify into a category four system later today, and emergency services have urged everyone in the path of the cyclone to start activating their emergency plans.

Islands and coastal areas of the western and southern Gulf of Carpentaria are expected to receive heavy rainfall today, which may lead to flash flooding.

As the cyclone approaches the coast, a storm tide between Port Roper in the Northern Territory and Karumba in Queensland may develop.

This could result in tides that are significantly higher than normal, damaging waves and minor flooding between Port Roper and Karumba.

Tides are also expected to be higher between Alyangula and Port Roper, with large waves that may produce minor flooding between the two areas.

Cyclone will bring heavy rainfall across Queensland

The system is forecast to start moving slowly eastwards back towards the Queensland coast during Thursday.

As it tracks east, it is likely to pass close to Port McArthur.

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The system is likely to cross the coast along the south-east Gulf of Carpentaria coast between Karumba and Pormpuraaw early Saturday morning, likely as a category four system.

The weather bureau expects the cyclone to weaken after making landfall, before making its way down Queensland's east coast, bringing heavy rainfall, potential flash flooding and destructive winds.

Queensland's state disaster coordinator Bob Gee said people both in the path of the cyclone and across the state needed to plan ahead.

"For those people that are out there camping, or in caravan parks, or planning to travel over the weekend, can you just watch the weather, have a plan, and please talk to others to let them know where you're going," Mr Gee said.

"For the entire community from Cairns right down into the Sunshine Coast and Brisbane, if we're moving over the next week can we have a lot of thought about that."

Premier Annastacia Palaszczuk said preparations had been made to deal with the severe storm.

She said the rain, expected to reach most parts of the state's east coast, could cause further damage in bushfire-affected areas.

"Once you have bushfires through an area, with large amounts of rain, there is then the potential for landslides," she said.

The system is forecast to move towards Queensland on Thursday, as seen from Gulf Country ( Twitter: QAS )

"[Areas of concern are] the road from Mackay up to Eungella. So of course we'll be speaking with the community there and we'll be making sure that the local disaster group meeting in Mackay keeps residents informed.

About 125 people moved to Borroloola's two public shelters yesterday, while no-one attended another cyclone shelter opened at Numbulwar.

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

People in the region should finalise their cyclone plans and preparations as soon as possible and take shelter as conditions deteriorate.

Boaties fishing in Gulf rescued

Northern Territory Police rescued three fishermen in distress on a boat near South West Island in the Gulf of Carpentaria on Wednesday afternoon.

Duty Superintendent Shaun Gill said a jet was deployed from Cairns and a helicopter from Katherine to locate the boaties, after their EPIRB was activated.

Although the helicopter was forced to turn back due to bad weather, the jet found the stricken anglers.

"The message is quite clear: if you're thinking about going boating or doing anything like that in the Gulf, don't. Don't even think about it," Superintendent Gill said.

Meanwhile, a squall line — a line of thunderstorms — brought severe winds and rain to the Top End last night, prompting the Bureau of Meteorology to issue a warning at 10:00pm.

Sorry, this video has expired Storm clouds form over Borroloola

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.