Dutch police tweeted at about 19:30 (18:30 GMT) that they were investigating a "suspicious situation".
Part of the airport, which is one of Europe's busiest, was closed to passengers as officials investigated.
But after people were evacuated from the plane, Air Europa announced a pilot had accidentally set off an alert.
"False alarm. In the flight Amsterdam-Madrid this afternoon was activated, by mistake, a warning that triggers protocols on hijackings at the airport," the airline tweeted.
"Nothing has happened, all passengers are safe and sound waiting to fly soon. We deeply apologize."
Shortly before their announcement, Dutch military police confirmed all passengers and staff had been safely evacuated from the Madrid-bound flight.
Images posted on social media showed parts of the airport's D-pier cordoned off to the public, with passengers waiting around for information.