The window dropped on the school grounds, slightly injuring one boy, news agency Kyodo said.
The southern island of Okinawa hosts the largest US military presence in Japan.
Over the past years, a number of accidents and crimes have led to growing local opposition to the US base.
According to the Reuters news agency, Japan's Chief Cabinet Secretary Yoshihide Suga said "this sort of incident creates anxiety not only among those involved with the school but the people of Okinawa and should never happen".
