Yoon Young-Doo acknowledged that the 46-year-old pilot, Lee Kang-Kuk, was training aboard the Boeing 777, but said he was accompanied by an experienced co-pilot with two other staff in the cockpit as well.
While Lee had just 43 hours of experience in flying that model of plane, he has more than 9,000 hours of flight time under his belt, Asiana said.
"Such speculation (about inexperience) is intolerable and it's contrary to the facts," Asiana CEO Yoon told reporters.
The South Korean airline's boss added that Lee, who was in charge of the landing the plane which burst into flames as it hit the runway in San Francisco, was undergoing a "very regular type of training that is done by all other airlines around the world".
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The pilot was attempting his first 777 landing in San Francisco. He had previously landed there flying 747s from 1999 through 2004, the airline said.
His trainer was an experienced pilot with more than 12,000 hours of flight time, it said.
Asiana's chief has previously dismissed an engine or mechanical problem as being the cause of the crash, which left two dead and 182 others injured.
"I feel so much pain both physically and mentally," the woman told Yonhap news agency.
"My whole body aches."
Another passenger who arrived at Seoul's Incheon airport was carried on a stretcher to a waiting ambulance outside the arrival gate, Yonhap reported.
The South's transport ministry said it would take months to identify the cause of the accident, although initial inspections showed the plane's tail struck a sea wall at the end of the runway.
Asiana said the airliner, purchased in March 2006, had received repairs for oil leaking from an engine early last month but this was not a factor in the crash.