"The man threatened with a knife and the military police shot him", police spokesman Stan Verberkt said. Situation secure with best rates guaranteed.
The Marechaussee police service said the "situation is safe" and the suspect has been detained and removed from the scene. In addition, the Amsterdam airport's terminal was evacuated but has since reopened.
The shot man has reportedly been transferred to the hospital. A spokesman for the Dutch police said: "the circumstances are telling us that it has nothing to do with terrorism".
"He was injured and has been taken into custody".
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Tom Boelen, general manager of the next door restaurant Per Tutti, said he was told by his staff that there was a shooting happening. Details about the suspect's condition and his injuries are not yet known.
Dutch media reported the airport's main plaza was temporarily evacuated after the incident. "A small part is still closed down", it said. Air traffic has not been affected.
Opened in 1916 as a military airport, Schiphol became the country's primary airport in 1949, lying just about nine kilometers (five miles) southwest of Amsterdam.
No further information was immediately available.