"This afternoon a man came into the office of the Marechaussee (military police) here at Schiphol and threatened my colleagues with a knife," said police spokesman Dennis Muller.
"He was shot in the leg and taken to hospital in Amsterdam."
The incident triggered panic on the airport's vast plaza, which is criss-crossed by thousands of people every day making their way to and from the departures and arrivals halls.
A worker at a fast food shop told AFP she saw a man "waving a knife around" before hearing a single shot.
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Schiphol airport is one of Europe's top five busiest air hubs, handling a record 63.6 million passengers in 2016, up from 58 million in 2015.
Muller told AFP the military police did not know the man or anything about him.
"He seemed to be a confused person," Muller said, adding "our investigators are on the scene to try and determine exactly what his motives were."
The cavernous plaza, where trains arrive underground and where people can also stop to shop or eat in a large commercial area, was briefly evacuated.
"Air traffic is experiencing no further consequences," it added.
AFP correspondents saw that the police office and the Starbucks coffee shop next door had been cordoned off with red-and-white tape, and green-and-white screens guarded by heavily armed military police had been erected to shield the area from curious onlookers.
"At this stage, the situation has returned back to normal. Trains are running again, and planes are departing from the airport," Muller said.
In a mobile phone video broadcast on the Dutch broadcaster NOS, a man is heard shouting "there are shots being fired" then the sound of three shots echoing in the plaza.
One cafe worker interviewed by the NOS said everyone "was in a terrible panic" and some of the clients had even sought shelter in their kitchen.
Tom Boelen, general manager of next door restaurant Per Tutti, said he was told by his staff that there was a shooting happening.
"They heard several shots and some of them ran for the exit, while others ran into the kitchen," he told AFP.
Opened in 1916 as a military airport, Schiphol became the country's primary airport in 1949, lying about nine kilometres southwest of the Dutch capital, Amsterdam.
The Netherlands has so far been spared from the slew of terror attacks which have rocked its closest European neighbours in past years.
But amid a number of scares in recent months, and reports that people linked to some of the attacks may have crossed briefly into the country, concerned top Dutch security and intelligence officials have been keeping a wary eye on events.
Schiphol was the scene of a late-night evacuation in April 2016 just a few weeks after the Brussels metro and airport suicide bombings when a drunken, homeless man sparked a security scare at the Dutch airport.