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Tsutomu Yamaguchi was in Hiroshima on a business trip on 6 August 1945 when a US plane dropped the first atomic bomb.
He suffered serious burns and spent a night there before returning to his home city of Nagasaki just before it was bombed on 9 August.
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'Horrifying history'
It was already recorded that Mr Yamaguchi had survived the Nagasaki bomb but on Tuesday officials recognised that he had been in Hiroshima as well.
Certification as a hibakusha or radiation survivor qualifies Japanese citizens for government compensation, including medical check-ups, and funeral costs.
His double dose of atomic bombs, however, does not mean Mr Yamaguchi's compensation will increase, a Nagasaki city official said.
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"It can tell the younger generation the horrifying history of the atomic bombings even after I die."
About 140,000 people were killed in Hiroshima and 70,000 in Nagasaki.
Many survivors fell sick with radiation-related illnesses, including cancers, for years after the bombings.