According to Japan's non-nuclear principles and Japanese-US security arrangements, Tokyo should refuse to allow a nuclear-armed US ship passage through its territory.
"But in reality, I'm afraid it can be possible" for a nuclear-armed US military ship to sail through Japanese territory waters in case of emergency, Defense Agency Director General Fumio Kyuma told a parliament session.
"It would be unavoidable in the event of an emergency," Kyuma added.
A nuclear debate has been heated here since ruling party officials openly called for the country to hold a frank debate on whether to develop nuclear weapons after North Korea's nuclear test on October 9.
Prime Minister Shizo Abe has downplayed a brewing debate in his party on Japan's own nuclear option, saying "we will stick to the three-point non-nuclear principles."
Abe referred to the 1967 policy under which the only nation to suffer a nuclear attack has refused the possession, production and presence of nuclear weapons on its soil.