The pilot of the F-16 Fighting Falcon ejected before the supersonic aircraft came down in the White Sands National Park, Holloman Air Force Base said on its Facebook page.
The sole pilot, who was not identified, was transported for medical treatment.
"All non-emergency personnel should avoid the area to prevent possible exposure to hazardous chemicals onboard the aircraft," Holloman AFB said.
Emergency response teams were sent to the area and a probe into the crash had begun.
"An investigation conducted by a board of qualified officers is underway to determine the cause of the incident," the statement said.
The national park is surrounded by the White Sands Missile Range, a giant US military-run area where hundreds of weapon and missile tests are carried out every year.
The range was the site of the Trinity Test, the first-ever detonation of an atomic bomb, which was carried out in 1945.
The F-16 Fighting Falcon is a single-engine supersonic plane that was initially developed for the US military in the 1970s.
Hundreds remain in service.
The White Sands National Park is a 230 square-mile (600 square-kilometer) expanse known for gypsum-filled sand dunes that rise up to 60 feet (18 meters) in the air.
It attracts hundreds of thousands of visitors every year.
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