Air Europa said in a tweet on Wednesday night that the scare that sent emergency services rushing to Schiphol was a false alarm.
The carrier says a warning that triggers hijack protocols at airports "was activated, by mistake."
It adds that all passengers "are safe and sound waiting to fly soon. We deeply apologise."
Dutch military police at the airport. Photo / via Twitter
Reports on Twitter suggested three men armed with knives were trying to hijack an outbound flight - and there are suggestions hostages have been taken on board a plane.
Local reports have said the situation has now "been ended", but it is unclear what has happened to resolve the incident.
The incident reportedly took place on board an Air Europe plane to Madrid with at least 27 people thought to be on the flight.
A crew member of the departing flight activated a hijacking alert, according to Dutch broadcaster NOS.
BREAKING: #AirEuropa says the emergency situation at #Amsterdam’s #Schiphol Airport was triggered by one of its pilots accidentally setting-off the hijack alarm. The airline has “deeply apologised” for the incident. pic.twitter.com/kDGr8Ranko
Emergency services issued a so-called Grip 3 report. This happens with "an incident or serious event with major consequences for the population", reports De Telegraaf.
Images showed crowds of people in the airport and armed police behind a cordon.
Reports suggest men armed with knives were trying to hijack an outbound flight. Photo / via Twitter
Schiphol Airport's official Twitter account tweeted: "The Royal Netherlands Marechaussee is currently investigating a situation on board of a plane at Amsterdam Airport Schiphol. We keep you posted."
Dutch military police are responding to reports of a suspected hijacking onboard a plane at Amsterdam Schiphol airport. Photo / via Twitter
Amsterdam's Schiphol airport. Photo / via Twitter
One passenger said: "Masses of people have just been asked to move back further behind the security cordon."
Another passenger told MailOnline: "Nobody knows what is happened here, there was a lot of screaming going on and armed police running about.
"It's quite a frightening experience as we are behind a cordon unable to move for our own safety as police is everywhere."
The Royal Netherlands Marechaussee is currently investigating a situation on board of a plane at Amsterdam Airport Schiphol. We keep you posted. https://t.co/AxwMZ7CZtT
Schiphol is one of the busiest transport hubs in Europe, handling more than 70 million passengers a year.
There is currently an emergency situation at Amsterdam-Schiphol airport. The situation is causing flights at the D and E, even number gates to be directed to hardstands. The airport is operating. No further info on nature of emergency.https://t.co/sVZWoPdKLKpic.twitter.com/oElGwfwaKA
