The emergency prompted the authorities to evacuate part of Schiphol, one of Europe's busiest airports.
There are no reports of any other injuries. "Situation safe", the Marechaussee police service said on Twitter. In a Tweet, the police said the man was "known to police in connection with previous violent incidents".
"He was injured and has been taken into custody", Verberkt added.
Dutch media reported the airport's main plaza was temporarily evacuated after the incident.
"Man shot by the military police at Schiphol Airport after he threatened [people] with a knife". Trains were briefly ordered not to stop at the airport's underground station.
The motives and the condition of the suspect remain unknown, but local media report that he had been acting aggressively and broke a window.
In a tweet the airport said a small part remained closed and that air traffic was not impacted.
The incident is not being treated as an extremist attack, spokesman Stan Verberkt said.
"Schiphol Plaza has been re-opened to the public again".
One of the military policemen takes up a position behind a pillar as he moves in on the suspect.