Taiwanese carrier EVA Air has flown into a storm of controversy over its "risky" decision to operate most of its flights as scheduled at the height of a recent typhoon, with several planes landing at Taoyuan International Airport even as other airlines stayed away.

The airline has faced a barrage of criticism from social media users following unconfirmed reports that some of its crew were injured when strong turbulence hit the planes flying into Taoyuan on Tuesday, Taiwan media reported.

The Civil Aeronautics Administration (CAA) on Wednesday slammed the company for "recklessness", and said it would look into whether the airline had followed aviation regulations.

EVA Air on Wednesday apologised to passengers aboard the flights for the "inconvenience and discomfort" they experienced, but insisted that it gave those flights the go ahead as conditions at Taoyuan airport met safety standards.

The company also said that all its Tuesday flights followed safety protocols and did not endangered the lives of its crew and passengers. It denied that any of its crew members was injured .

Forty-five Eva Air flights were scheduled to land at Taiwan Taoyuan International Airport on Tuesday, when most schools and offices in Taiwan were shut as Typhoon Megi, packing winds of well over 160 kph, swept in from the Pacific. Hundreds of international flights were cancelled.

At least four people were killed and hundreds more injured in the ensuing storm.

But Eva landed 30 of its 45 scheduled flights at Taoyuan International Airport, including some which were initially diverted to Hong Kong and Okinawa but took off again and landed in Taoyuan, according to CAA data.

The United Evening News said EVA was not the only airline that allowed flights to approach the Taoyuan airport on Tuesday. A TransAsia Airways flight and a Malindo Air flight attempted to land at the Taoyuan airport, but failed and had to be diverted to other airports.

Company spokesman Ko Chin-cheng was cited by the newspaper as saying that it would be "convenient" to cancel flights when a typhoon approaches, but that airlines seek to minimise inconvenience to passengers.

For one thing, said Ko, it is "difficult" to accommodate passengers whose flights had been cancelled.

Diverting flights also pose extra costs to airlines, Ko said.

But some netizens said Eva set a poor precedent by flying during storms, giving "overbearing" passengers an excuse to criticise airlines for choosing to cancel flights during typhoons, Central News Agency reported.