Air Europa said the captain of its flight from the Dutch city to Madrid triggered the alert by mistake.
Dutch Prime Minister Mark Rutte told a meeting of his VVD party he may be called away because of the situation at Schiphol, according to the UK's Guardian.
A large contingent of authorities and officers were dispatched to the Schiphol Airport in Amsterdam on Wednesday night because of an incident on an aircraft.
All passengers and crew were safely removed from the plane, according to the Marechaussee.
"Nothing has happened, all passengers are perfectly waiting to fly soon", the airline said in a statement.
Dutch officials said earlier they had declared an incident or serious event with major consequences.
Reports on Twitter suggest men armed with knives were trying to hijack an outbound flight - and there are suggestions hostages have been taken on board a plane.
Emergency services have issued a Grip-3 report, De Telegraaf reported.
Photos shared on social media show areas of the airport cordoned off with police tape. Eyewitnesses reported that parts of the airport had been closed off and shared images of crowds and confusion.
However, passengers at the airport are reported a state of lockdown, and a heavy armed response presence.
It's great to know that we're all in safe hands when passing through one of Europe's busiest airports.