"Situation safe", police said on Twitter.
Shocked travelers fled when the man, who has not been identified, began threatening crowds with his knife.
Military police had tweeted: "Man at Schiphol shot at by the military police, after he made threats with a knife".
Passengers took to social media to describe the incident. There were no other injuries reported.
Schiphol is one of Europe's busiest airports and Friday is one of its busiest days of the week.
"The man threatened with a knife and the military police shot him", spokesman Stan Verberkt said, according to Sky News.
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"He was injured and has been taken into custody", Verberkt added. No details of his condition were released and a motive is unclear.
Heavily armed military police, wearing body armor and ski masks, patrolled Schiphol for four hours while the man's bags were checked.
The suspect has been detained and removed from the scene.
But the airport tweeted later that the plaza was "reopened to the public again".
A spokesman for the airport said the main plaza was evacuated and part of it is still closed off, but that the areas after check-in were operating as normal. "At the moment air traffic is not affected".
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