During an episode of comedy quiz show QI, which was broadcast in the U.K. last month (Dec10), the funnyman made a number of gags about Tsutomu Yamaguchi, who survived both the bombings of Hiroshima and Nagasaki in 1945.
Fry called Yamaguchi "the unluckiest man in the world" for escaping the Hiroshima bombing with minor injuries and then returning to his native Nagasaki shortly before the city was also attacked.
BBC chiefs have received a letter of complaint from officials at the Japanese embassy and they have now apologised for Fry's jokes.
A joint statement from the corporation and the show's Talkback Thames production company, reads, "We are sorry for any offence caused. QI never sets out to cause offence with any of the people or subjects it covers. However, on this occasion, given the sensitivity of the subject matter for Japanese viewers, we understand why they did not feel it appropriate for inclusion in the programme."
Fry adds in a post on Twitter.com, "I'm coming to Japan the week after next as it happens, and I'll certainly let my regret (be) known (if they let me in!)."
Yamaguchi is the only person to have been formally recognised by the Japanese government as having survived both atomic bombings, which killed more than 200,000 people. He died last year (10) at the age of 93.