There were 315 people aboard the Boeing MD-11, which belonged to the Taiwan- based China Airlines.
Waiting passengers at the airport witnessed the crash. "I saw the plane, like a fireball coming down," said Toshi Hoshino, a businessman from Osaka, Japan, who was changing planes in Hong Kong. "The right wing hit the ground first. The left side of the body then followed."
"The flight was on fire before it landed," said an American businessman from Portland, Oregon, who saw the disaster from an airport restaurant. "It left a trail of fire, five or six times as long as the plane. They seemed to have problems containing the fire. It was so windy." He said the plane was surrounded by fire engines and ambulances but it took five to 10 minutes to bring the flames under control.
Tropical Storm Sam, which saw winds gusting to 85mph, hindered the rescue of passengers from the burning plane at Chek Lap Kok airport.
Flight 642, arriving from Bangkok, Thailand, was thrown off balance by "an overly hard side wind", according to Scott Shih, a spokesman for China Airlines. He said the plane's captain had radioed the Hong Kong control tower to report that a fire had broken out on board and was given immediate permission to land. Airport authorities closed Chek Lap Kok as well as an express train that runs between downtown Hong Kong and the airport.
Two people - a man and a woman - were killed, a Hong Kong government spokeswoman said. Hong Kong's Yan Chai Hospital said the woman was aged 31. At least 65 people were taken to hospitals, 20 of them seriously injured.
Questions are certain to be asked about why the aircraft was flying in a tropical storm. Officials said 20 incoming and 16 outgoing flights were delayed, diverted or cancelled during the storm. Officials said that in Hong Kong itself the weather caused minor injuries to 100 people from uprooted trees and flying debris.
Many of the passengers are believed to have been Thai citizens. There were also about 80 Portuguese tourists aboard, said a Hong Kong travel agent, Sardy Tong, who had come to the airport to meet them.
Mr Tong said that China Airlines had advised him earlier in the day that the flight would not be coming in, then he got a phone call saying it had taken off. "They shouldn't even have let the plane fly," he said.
It was the worst accident since the $9bn airport opened in July last year. China Airlines have had a number of serious disasters. Last year a China Airlines Airbus crashed killing 196 people. In 1993, a China Airlines Boeing 747 veered off a runway at Hong Kong's old Kai Tak airport and belly-flopped into the sea, injuring 22 people.