Dutch F-16 fighters were scrambled to intercept the aircraft, en route from Malaga, Spain.
Once it landed at Schiphol it was boarded by armed security forces who discovered the false alarm.
A miscommunication between the pilot and the control tower reportedly triggered the confusion.
"There was never any danger. There was a lack of communication between the pilot and the tower and the airport has activated the security protocol," a spokeswoman for Spanish carrier Vueling told Reuters news agency.
Dutch broadcaster NOS spoke to a passenger who said the situation on board had been "calm".
It was the second drama at the airport on Wednesday.
Earlier, part of Schiphol was been closed and flights delayed after a suspected World War II bomb was discovered by workers digging near Pier C, which connects the main plaza with Departure Hall One.