The waves, which were 7 metres (23 feet) high in some areas late last week, struck large parts of Indonesia, the Maldives, Thailand and Western Australia.
There was no official warning about the freakish waves that killed at least one person, damaged hundreds of homes and displaced thousands of people across Indonesia. Homes and fishing boats were also damaged in Thailand and the Maldives.
Weather officials said the waves were the result of an accumulation of winds in one spot on the ocean, but were looking at why they were so intense.
Triwahyu Hadi, a meteorology expert at the Bandung Institute of Technology, said the phenomenon was likely caused by Kelvin waves, giant waves caused by a surge of irregular wind patterns in the Indian Ocean.
He said it could have easily been predicted because such waves commonly occurred around this time.
"However, we didn't expect the waves to be of this size, that's why we need to analyse the other factors first before arriving at a conclusion."
The European Space Agency said the huge waves were generated by intense storm winds in the Southern Ocean on May 8.
The waves originated south of Cape Town in South Africa and travelled northeast for nearly 4,000 km (2,500 miles) over three days before slamming into Reunion Island on May 12, said the ESA's Web site, (www.esa.int/esaEO/SEMAKIV681F_economy_0.html).
Using satellites, French researchers tracked the huge swell as it travelled northeast, hitting first Reunion, Madagascar, the Maldives and finally Indonesia.
Initial forecasts were for waves only a couple of metres in height, said French researchers on the ESA Web site, but due to the large time period between swells, around 19 seconds, the intensity of the waves was much greater.
"Swells are still surprise factors, which can unfortunately be deadly," Bertrand Chapron of IFREMER, the French Research Institute for Exploitation of the Sea, said on the ESA Web site.
Australian surfing Web sites started monitoring the huge swell from early last week as it rolled out of the Southern Ocean, creating around three-metre swells in Madagascar and the Maldives, which flooded some low-lying islands.
Australia's big surf breaks around Margaret River in southwest Australia were pounded by waves up to 20 feet as the huge westerly swell hit the coast.
Huge waves later hit Bali, giving surfers adrenalin-fuelled rides, but washing away beachside restaurants and fishing boats.
"This month there has been an astronomically extreme phenomenon. The tidal waves were caused by a combination of several factors, including winds travelling at extreme speed in the Indian Ocean," said Widada Sulistya, head of Meteorological and Geophysical agency in Bali.
The crashing waves brought back painful memories of the Indian Ocean tsunami in December 2004, which killed about 170,000 people in the Indonesian province of Aceh alone.
Sukabumi regency in West Java was one of the areas worst hit last week, with more than 600 people fleeing their homes.
On Monday, foreign and local tourists returned to the sea on Bali's famous Kuta beach, while fishing boats also set out again.
In Thailand, strong winds and high tides generated a storm surge along the Andaman Sea coastline, with waves as high as 5 metres pounding Phuket beaches.
"Some homes and fishing boats were damaged," Smith Dharmasaroja, head of Thailand's National Disaster Warning Centre, told Reuters. There were no reports of injuries.
In Bangkok, workers laid 400,000 sandbags in 14 flood-prone areas along the Chao Phraya river, which rose as much as 2 metres at the weekend due to high tides, the Thai News Agency said. (Additional reporting by Michael Perry in Sydney, Darren Schuettler in Bangkok and Ahmad Pathoni and Adhityani Arga in Jakarta)
- Reuters - Thomson Reuters Foundation
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