The news came as security in the Japanese capital was dramatically ramped up, with 16,000 police officers deployed in readiness for the first state visit by a US president in nearly two decades.
A Skymark Airlines employee at the busy Haneda airport in Tokyo lost a piece of paper bearing security codes on Sunday afternoon, a transport ministry official said.
The note was found on the floor of the departure lobby around half-an-hour later, he said.
In the city proper, a heightened police presence has made the sight of officers patrolling streets and stations commonplace.
Local media said a full third of Tokyo's police force had been pressed into service for Obama's two-night visit, which begins tomorrow.
Left luggage lockers and rubbish bins have been sealed in some stations and thousands of security cameras have been put into operation.
Obama is due to leave Tokyo bound for Seoul on Friday morning.
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