The islands, hugely popular with holiday-makers especially during the peak Christmas and New Year season, have emptied out since Wednesday as tourists packed onto ferries bound for the southern Thai mainland, with swimming banned and boats set to suspend services.
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Pabuk, Thailand's first tropical storm in the area outside of the monsoon season for around 30 years, is poised to batter Koh Phangan and Koh Tao as well as Koh Samui on Friday night, before cutting into the mainland.
No official evacuation order has been given but tourists are leaving in droves.
"I think the islands are almost empty ... between 30,000 to 50,000 have left since the New Year's Eve countdown parties," Krikkrai Songthanee, Koh Phangnan district chief, told AFP.
The acting mayor of Koh Tao, one of Southeast Asia's finest diving spots, said boats to Chumphon on the mainland were crammed with tourists, but several thousand guests were still on the island likely to brave the storm.
Pabuk was packing winds of 104 kilometres per hour (65 mph) but was unlikely to intensify into a full blown typhoon, according to forecasters.
"But we expect waves as high as five or seven metres near the eye of the storm. Normally in the Gulf of Thailand there are only two metre high waves," Phuwieng Prakammaintara, director general at the Thai Meteorological Department, told reporters.
"It's difficult to predict the severity of the storm so people should comply with authorities' recommendations."
On Koh Samui, the closest of the trio of islands, a Russian man drowned on Wednesday after his family ignored warnings not to go into the sea.
"A family of three went swimming but the strong current caught a 56-year-old man who drowned," Police Captain Boonnam Srinarat of Samui Police told AFP.
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"Island officials anounced the warning and put up the red 'danger' flags ... but maybe the family did not think the situation was that serious."
Authorities on the island said they were preparing shelters for any tourists who decide to wait out the storm.
Pabuk, which means a giant catfish in Lao, is also expected to dump heavy rain across the south, including tourist hotspots in the Andaman Sea such as Krabi and the southernmost provinces bordering Malaysia of Pattani, Narathiwat and Yala.
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