The investigative report was released at the start of a daylong NTSB hearing that was called to answer lingering questions about the crash, not to conclude exactly what went wrong.
Though Lee was an experienced pilot with the Korea-based airline, he was a trainee captain in the 777, with less than 45 hours in the jet. He had not piloted an airliner into San Francisco since 2004, according to NTSB investigator Bill English.
So far, the investigation has not found any mechanical problems with the 777 prior to impact, although testing is ongoing, English said.
Lee told investigators that he realized others had been safely landing at San Francisco without the glide-slope indicator, an array of antennas that transmits a signal into the cockpit to help with the descent. That system was out of service while the runway was expanded. It has since been restored.
In his interview, the trainee said that while privately he was "very concerned" about his ability to do a visual approach, "everyone else had been doing (it), so he could not say he could not do the visual approach."
There were other indications that a culture of not acknowledging weakness and of deferring to a higher-ranking colleague contributed to the crash.
Lee told NTSB investigators that he did not immediately move to abort the landing and perform a "go around" as the plane descended because he felt that only the instructor pilot had the authority to initiate that emergency move.
A reluctance of junior officers to speak up had been an issue in past accidents, though industry training has tried to emphasize that safety should come first.
Lee also conceded that he was worried about his unfamiliarity with the 777's autoflight systems. He admitted he had not studied the systems well enough and thought that the plane's autothrottle was supposed to prevent the jet from flying below minimum speed as it drew near the runway.
But two other Asiana pilots who took an instruction class with Lee said that they were told that the throttle hold did not automatically re-engage under certain autopilot modes.
"This pilot should never have taken off," said attorney Ilyas Akbari, whose firm represents 14 of the passengers. "The fact that the pilot was stressed and nervous is a testament to the inadequate training he received, and those responsible for his training and for certifying his competency bear some of the culpability for the tragedy of this crash."
Lee told investigators that as he realized his approach was off, he was worried he might "fail his flight and would be embarrassed."
Another Asiana pilot who recently flew with Lee told investigators that he was not sure if the trainee captain was making normal progress and that he did not perform well during a trip two days before the accident. That captain described Lee as "not well organized or prepared," according to the investigative report.
Asiana's chief pilot told investigators that the airline recommended pilots use as much automation "as possible."
He also said that the airline told its pilots to turn off the 777's autopilots below 1,000 feet when making visual approaches to airports. But a former Asiana pilot told the board that Asiana pilots were rarely allowed to practice visual approaches on landing and that many trainee pilots "did not feel confident and did not want to make any mistakes."
The agency did not say whether Asiana's reliance on automatic landings was greater than the industry norm.
Recordings from the cockpit show Lee took the controls as the autopilot disconnected when the plane was about 1,500 feet above San Francisco Bay.
Lee insisted in interviews that he had been blinded during a critical instant before the botched landing by a piercing light from outside the aircraft. NTSB investigators repeatedly probed him about the light, but he was unable to pinpoint its origin or how it precisely affected him.
The instructor pilot said he never saw a bright light outside the aircraft.
According to a transcript of the Asiana plane's cockpit voice recorder, the crew did not comment on the jet's low approach until it reached 200 feet above the ground.
"It's low," an unnamed crewman said at 11:27 a.m.
In an instant, the plane began to shake.
At 20 feet, another crewman broke in: "Go around," he said. But It was too late.
NTSB investigators also raised concerns about a safety certification issue involving the design of Boeing 777's controls, warning that the plane's protection against stalling does not always automatically engage.
When the plane's autothrottle is placed in a "hold" mode, as it was during the Asiana flight, it is supposed to re-engage or "wake up" when the plane slows to its minimum airspeed.
But a pilot who oversaw the Boeing 787 flight tests for the Federal Aviation Administration told the NTSB that both the 787 and the 777 have the same anti-stall protection systems and that the wake-up system did not always work when tested at minimum speeds.
Boeing's retired 777 chief pilot, John Cashman, underscored that auto controls are not designed to replace pilots.
"The pilot is the final authority for the operation of the airplane," he said.
Follow Martha Mendoza at https://twitter.com/mendozamartha .
Mendoza reported from San Jose, Calif. Associated Press Airlines Writer David Koenig in Dallas contributed to this report.