More than 700 people were supposed to be flown to Darwin by the Australian Defence Force, but severe weather in the area hampered the rescue mission.

Chief Minister Eva Lawler said the Government was now working with the local emergency management team "to keep the community safe".

"There are enough buildings in Borroloola that are rated to withstand a category 3 cyclone to keep the community safe.

"These include the police station, the health centre and dozens of homes in the community.

"The ADF will land at Borroloola when safe to do so."

The Bureau of Meteorology said Severe Tropical Cyclone Megan is expected to make landfall as category three system in the evening of Monday, January 18.

"The very destructive core of Megan, with wind gusts up to 200 km/h, is now impacting the Sir Edward Pellew Group and will extend to adjacent coastal areas between Bing Bong and the NT/QLD border throughout the day as the system slowly crosses the coast today," the Bureau said.

Destructive gusts to 140 km/h are forecast to extend to inland areas near the forecast track southeast of Borroloola.

Heavy to locally intense rain is expected along the southwestern Gulf of Carpentaria coast during today and may even occur about parts of the Gulf Country in Queensland, and is likely to extend to the Carpentaria and northern Barkly districts as the system is expected to move inland during Tuesday.

Coastal residents between Bing Bong and the Northern Territory/Queensland border are specifically warned of a dangerous storm tide as the cyclone centre crosses the coast.

"Tides are likely to rise significantly above the normal high tide, with damaging waves and dangerous flooding," the BOM warned.

Abnormally high tides are expected over remaining parts of the southern Gulf for the next few days, and will likely rise above the normal high tide at times.