Asiana Airlines Flight 214 from Seoul crashed at 11.27 a.m. (12.07 a.m. Sunday India time) and came to rest on the side of one of the airport's four runways, San Francisco Chronicle reported citing officials.
Federal Aviation Administration spokesperson Lynn Lunsford said the plane appeared to make impact short of the runway - its tail was obliterated, leaving a trail of debris.
There were 291 passengers and 16 crew members aboard. Two people were killed and 82 were taken to area hospitals, the newspaper said citing San Francisco Fire Chief Joanne Hayes-White.
Airport spokesperson Doug Yakel said at an evening press conference that only one person was unaccounted for.
There was no immediate indication of what caused the crash, but an FBI special agent cited by the Chronicle said there was no indication it was a terrorist act.
San Francisco General Hospital spokesperson Rachael Kagan said 49 of the injured people at area hospitals were in critical condition.
Video footage of the plane taken by news helicopters showed the plane on its belly. The cockpit was intact but the top of the fuselage from the front to the wings had burned away. The jetliner's tail section was gone.
The cause of the crash was not known, but some witnesses cited by the Chronicle said the tail slammed into the ground first. Aerial news footage showed debris, including parts of a wheel assembly, extending from an embankment at the front of the runway.
The National Transportation Safety Board said its investigators were en route to San Francisco, and would be looking into the incident with officials from Boeing and Korean accident investigators.
The airport was closed to all air traffic for more than three hours after the crash, and flights were diverted to Oakland, San Jose and Sacramento. Two runways reopened shortly after 3.00 p.m.