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.