The mayors of both cities have been informed of the decision by Japanese Olympic boss Tsunekazu Takeda and advised to consider individual bids.
A proposal by Hiroshima and Nagasaki to table a joint bid for the 2020 Olympics has been rejected by the Japanese Olympic Committee (JOC).
A senior JOC official told Reuters on Friday the mayors of both cities had been 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 said.
"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 — in Tokyo earlier on Friday and refused to rule either venue out of the running.
"Hiroshima and Nagasaki both have a very good chance of staging an Olympics on their own," Takeda told reporters.
Tokyo, which lost out to Rio de Janeiro in October's International Olympic Committee (IOC) vote for the 2016 Games, is also in contention to become Japan's 2020 bid city.
The identity of Japan's bid city for the 2020 Summer Games could remain a mystery until 2011, Nakamori said.
"The IOC told us there was no need to rush a decision," Nakamori told Reuters. "They also suggested that if an African candidate emerged for 2020 they would be very strong contenders."
Tokyo governor Shintaro Ishihara has said the Japanese capital, Asia's first Olympic host city 45 years ago, has a "civic duty" to reapply.
The city secured a contingency fund of $4 billion for the 2016 Games, although JOC officials were said to have favoured a bid for 2020 from the start.
Hiroshima and Nagasaki had planned a joint bid to demonstrate their commitment to abolishing nuclear weapons.
Rio won the October 2 IOC vote for 2016, defeating Chicago, Madrid and Tokyo. London will host the 2012 Summer Games.
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