"We are sorry for any offense caused," the statement by the BBC and production company Talkback Thames said.
The latest apology came after media reports about the program generated strong reactions in Japan.
Earlier the program's producer sent a message to the Japanese Embassy and some viewers who protested about the show, called "QI," saying they "greatly regret it when we cause offence."
The BBC and Talkback Thames said in the statement, "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 program.
The BBC uploaded the part of the program in question on Internet video-posting site youtube.com, making it available for viewing all over the world. Comments, both from supporters and critics, surged yesterday night to over 1,000 from dozens up to Thursday.
The Japanese Embassy in London lodged a protest against the BBC and the TV production agency, saying that they insulted Tsutomu Yamaguchi, who survived both the bombings in Hiroshima and Nagasaki cities, in the show aired December 17.
The BBC said it will be sending a letter to the embassy shortly in reply to the embassy's protest.
The host on the show explained that Yamaguchi was badly burned by the atomic bomb when he was in Hiroshima on business and said, "Even though the atom bomb fell, the trains were working. So he got on a train to Nagasaki and a bomb fell again," drawing laughs from the show's personalities and the audience.
Yamaguchi died last January at age 93.
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