Sources close to O'Keefe's family told NBC News O'Keefe has a broken pelvis and other broken bones, but is expected to live. His son also survived the crash near Dillingham, Alaska, according to reports.
Five of the nine passengers on the plane are believed to be dead.
The Alaska National Guard was called to the scene on Monday night, but rescuers had trouble reaching the victims because of poor visibility. The National Transportation Safety Board has sent an investigative team to the crash site, according to the Associated Press.
O'Keefe, chief executive officer of EADS North America, served as NASA administrator from December 2001 to February 2005, overseeing the agency at the time of the Columbia space shuttle disaster. He also was deputy director of OMB in 2001, and acting secretary of the Navy from 1992 to 1993.