Some 700 residents in the community of Borroloola, inland from the Gulf of Carpentaria in the Northern Territory, were meant to leave the area but RAF aircraft are unable to land.
The category three cyclone has moved faster than anticipated and the eye of the severe weather system is expected to only be about 100km from the community, Fannie Bay MP Brent Potter told reporters on Monday.
"The weather conditions don't permit the aircraft to safely land and take people out of that location," Mr Potter said.
"That's the determination of the RAF pilots and we have to take their advice, they've been trying to leave and they can't do it."
He said residents could shelter at the police station, health facility or 40 dwellings capable of withstanding a category three system.
The cyclone was expected to cross land on Monday afternoon, bringing gusts of more than 200 km/h and heavy rainfall.
The territory's police commissioner Michael Murphy urged residents in Borroloola to listen to authorities on the ground.
"We're confident that the infrastructure there will be sustained throughout the night but we've got to take this really seriously," he said.
Groote Eylandt residents were hit with almost 600 millimetres of rain over the weekend as Megan made its way over the remote island communities.
Severe Tropical — Bureau of Meteorology, Australia (@BOM_au) #CycloneMegan is expected to cross the south-western #GulfofCarpentaria coast today with wind gusts up to 200km/h. Heavy rainfall is likely. Tides likely to rise significantly with damaging waves and dangerous flooding. Latest: https://t.co/4W35o8i7wJ. pic.twitter.com/8B2b7hqMjOMarch 17, 2024
The wharf on the GEMCO manganese mine has been damaged alongside the highway connecting communities.
Water and power outages have also been intermittent on the island.
The weather system intensified to a category three on Sunday with the Bureau of Meteorology warning there was a 20 per cent chance of it developing into a category four by Monday night.
"Severe Tropical Cyclone Megan is beginning to impact the southwestern Gulf of Carpentaria coast," the Bureau of Meteorology advised at 8pm (ACST) on Sunday.
The cyclone was forecast to hit the NT coast on Monday evening with a warning area spanning hundreds of kilometres - from Alyangula on Groote Eylandt in the NT to the Queensland border and inland to Borroloola, the McArthur River Mine and Robinson River.
"There is a moderate chance that this system could develop into a category four tropical cyclone," the bureau's Shenagh Gamble said on Sunday.
Severe Weather Update: Severe Tropical Cyclone Megan to make coastal crossing later today. Video current: 8:30am ACST 18 March 2024. For the latest forecasts and warnings go to our website: — Bureau of Meteorology, Australia (@BOM_au) https://t.co/4W35o8iFmh pic.twitter.com/Xquxg4tqK2March 18, 2024
The core of the cyclone has been called destructive, bringing wind gusts of up to 220km/h and rainfall totals of between 300 and 400mm.
Ms Gamble said the cyclone would likely remain a category three when it made landfall on Monday but could intensify if it slowed down before then.
Possible rainfall totals of between 150 and 200mm and wind gusts of up to 110km/h were forecast in the other hundreds of kilometres of warning zone and dozens of towns.
Flood watches are in place for the Carpentaria to Arnhem and Barkly.
The bureau said the flood warnings could expand as the cyclone hits the coast.
The weather system is expected to return to a tropical low as it heads further inland on Tuesday and Wednesday.
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