The mayors of both cities were informed of the decision by Japanese Olympic boss Tsunekazu Takeda and advised to consider individual bids.
"JOC president Takeda conveyed to them we must uphold the Olympic charter so co-hosting is not possible," the JOC's Olympic cooperation director Yasuhiro Nakamori told Reuters on Friday.
"It's possible Hiroshima could make a solo bid. The city staged the 1994 Asian Games. But it would be a bit difficult for Nagasaki to stage such a big international event." Takeda held talks with the mayors of Hiroshima and Nagasaki -- the only cities to have suffered a nuclear attack.