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.
No other injuries were reported.
"Situation is under control".
The incident is not being treated as an extremist attack, spokesman Stan Verberkt said.
Military police shot the man after he threatened a crowd this afternoon.
The military police said on Twitter that the man had been overpowered and taken away.More news: Sonia retiring only as President, not from politics : Congress
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Schiphol airport, just outside Amsterdam, is one of Europe's five busiest airports.
He was shot by military police, according to a tweet from Dutch police. 'He was injured and has been taken into custody'.
Verberkt told The Associated Press that "the circumstances are telling us that it has nothing to do with terrorism".
The motives and the condition of the suspect remain unknown, but local media report that he had been acting aggressively and broke a window.
But the airport tweeted later that the plaza was "reopened to the public again".
Videos on social media showed what appeared to be the suspect being taken out of the airport in a stretcher. Air traffic has not been affected.