China is holding its largest-ever military exercises around Taiwan and has vowed to seize it by force if necessary.
The US House Speaker Nancy Pelosi's visit to the self-ruled island sparked a show of military might despite stern warnings from Beijing.
Pelosi's plane touched down in Japan on Thursday for the final stop on her Asian tour.
AFP reporters saw the aircraft land at Yokota Air Base in Tokyo, with Pelosi arriving from South Korea.
Parts of Japan's southernmost island region of Okinawa are close to Taiwan. Kishi said that it was the first time that Chinese ballistic missiles had landed in Japan's EEZ.
The EEZ extends up to 200 nautical miles from Japan's coastline, beyond the limits of its territorial waters.
Kishi said the figure of nine missiles fired was an assessment by the Japanese side, and that the five appeared to have landed southwest of Okinawa's Hateruma island.