The roof gave in as heavy wind lashed the building on Tuesday night and parts of it landed on runway, official media here reported today.
The incident raises doubts on the landmark building's resilience, state-run China Daily said in a report.
Passengers at the airport's third terminal said that they saw white and yellow foam composites flying outside the building windows.
"Though I stood pretty far away, I could see a part of the roof was torn open. The white foam composite was everywhere, even on the runway," a passenger surnamed Li said.
Designed by British architect Norman Foster (known for working on projects such as the Millennium Bridge in London) and Beijing Architectural Design and Research Institute, T3 was opened in 2008 - the biggest standalone terminal building in the world then.
The airport officials said the strong wind, moving at a speed of 24 meters a second, lifted some of the metal plates on the roof of the terminal's D section.
But the damage has not interfered with flight schedules by Wednesday noon and it was quickly repaired by workers, the airport said its official micro blog at Weibo. com, the Chinese version of Twitter.
This is the second such incident in one year.Last December about 200 square meters of the roof was damaged, compared to its total area of 320,000 square meters.
The unexpected roof damage, as well as big snowfalls in other cities that day, caused widespread disruption for flights.
Incidents of strong winds damaging the terminal roof twice within the space of a year have made people skeptical about its quality, the Daily report said.
"How could Hong Kong's Chek Lap Kok Airport, also designed by Norman Foster, withstand typhoons so well throughout the past decade?" asked a netizen from Shenzhen at Weibo.com.
Shao Weiping, executive chief architect of Beijing Architectural Design and Research Institute, who had a role in designing T3, believed that the torn roof was not caused by design flaws.