The board said in a preliminary report that investigators interviewed the controller, a supervisor and others involved in the Oct. 19 incident in Long Beach, California. It did not comment on those interviews.
The incident is among the latest in a number of recent cases in which planes came unnecessarily close due to errors by air traffic controllers or pilots.
The NTSB said a controller told the crew of a four-seat Diamond DA40 to land on the main runway and stop short of an intersecting runway. About two minutes later, the controller cleared pilots of the Southwest Boeing 737 to land on the main runway, followed shortly by the Diamond crew telling the controller that they were stopped on the runway, as directed.
As they were completing their landing rollout, the Southwest pilots told the controller that there was another aircraft on the main runway, the NTSB said. Both planes taxied to their parking areas without further incident.