The threat forced a brief evacuation of parts of the airport, one of Europe’s busiest. But police said it was not being treated as a terror incident.
“The circumstances are telling us that it has nothing to do with terrorism,” police spokesman Stan Verberkt said.
Police said the man walked into the police service’s office at the airport and threatened staff with a knife. Officers shot him in the leg and arrested him before transporting him to a hospital.
A tweet from Dutch military police read: “Man at Schiphol shot at by the military police, after he made threats with a knife. Situation safe.”
The suspect remains in custody. No details of his condition were released and a motive is unclear.
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.
They added: “Schiphol Plaza was initially evacuated but is open to the public again. At the moment air traffic is not affected.”
Trains were temporarily not stopping, but are now going in and out of the airport station as normal.
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Video shared on social media shows a man being taken out of the airport on a stretcher.
Schiphol airport, just outside Amsterdam, is one of Europe’s five busiest airports. It handled a record 63.6m passengers during 2016.