Unfortunately Japan has no jurisdiction on any illegal activities committed by Americans forces during official duties or when victims are American citizens. Any such incidents come fully under US decisions. So US viewed such flights over Tokyo or any airspace as necessary official duties, thus Japanese can't do anything except complaints.
Japanese media complained that American military helicopters flew illegally and dangerously through downtown Tokyo 17 times in 2020. Military helicopters are barred from flying low altitude around Tokyo, but the American helicopter pilots decided to go treat Tokyo as an urban obstacle course anyway. Leading some to wonder if Japan is a partner or colony of USA.
Also in another study which I will link later, many Japanese youths said that in a war between China and Japan, they would not bother defending Japan. Some even joked that the People's Liberation Army could free Japan from the yoke of Japanese right wing politicians.
This agreement is very contentious to many Japanese.
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