It is printed with the English words "Patriotism", "Our History", "Liberation" and "Korea" and features reproductions of two photographs: one showing Koreans celebrating and the other showing the mushroom cloud of the atomic bomb that...
"We deeply apologize the viewers who were looking forward their performance", the station said.
TV Asahi said the Billboard-topping band would not be appearing on its programme "Music Station" after reaching out to BTS' record label about the T-shirt, which had caused controversy on social media ahead of the band's tour of Japan beginning next week.
It is believed that Jimin wore the shirt past year.
BTS apologised for the cancellation but made no reference to the T-shirt.
The "atomic bomb" T-shirt also featured Korean independence slogans.
Universal Music said it would continue to support BTS.
South Korea's local news outlets raised the possibility that the move was evident of anti-Korean sentiment in Japan.
The shirt is still available for purchase online.
The incident comes as ties between Japan and South Korea are once again strained over historical issues, with a court ruling holding Japanese firms liable for wartime forced labour claims roiling relations.
BTS member Jimin reportedly wore the shirt a year ago, on August 15, when Koreans celebrate the end of Japanese occupation in 1945.
Japan became the first nation to suffer an atomic bombing on 6 August 1945, at Hiroshima.
Furthermore, Fuji TV's 'FNS Music Festival' scheduled for December 5 and December 12 has also made a decision to reject the idea of inviting K-Pop group BTS to this year's programs, even though the station was previously considering the option.