On Saturday, Ryu Matsumoto allegedly took 90,000 yen in cash that a passenger had placed in a tray during baggage screening at a domestic terminal checkpoint, The Mainichi reported.
The passenger noticed missing money and reported it to another inspector.
Surveillance footage later showed Matsumoto acting suspiciously, police said.
Police said he admitted to the charge and told investigators he had stolen cash on 70 to 80 occasions since around August, totaling roughly 1.5 million yen, according to The Japan News.
Matsumoto, who worked as a guide at the checkpoint, admitted that he pretends to adjust trays while secretly pocketing cash and hiding it inside the cardboard tubes of replacement toilet paper rolls in a nearby restroom.
Haneda Airport, located less than 30 minutes south of central Tokyo, was named the world's cleanest airport this year by Skytrax, and is known for its immaculate floors, seating areas, public spaces, and washroom facilities.