The Rape of Nanking has caused controversy in Japan. Los Angeles Times staff writer, Sonni Efron, reported that Chang was also criticized by both Japanese "ultranationalists", who believe that the massacre in Nanjing never took place, and Japanese liberals, who "insist the massacre happened but allege that Chang's flawed scholarship damages their cause". Associate Professor David Askew of Ritsumeikan Asia Pacific University stated that Chang's work dealt a "severe blow" to the "Great Massacre School" of thought, which advocates for the validity of the findings at the Tokyo Trials, the tribunal convened to try the leaders of the Empire of Japan for crimes committed during World War II. Askew further argued that "the Great Massacre School has thus been forced into the (unusual) position of criticising a work that argues for a larger death toll."
Following the publication of The Rape of Nanking, Japanese critic Masaaki Tanaka had his 1987 book on Nanking translated into English. Entitled What Really Happened in Nanking: The Refutation of a Common Myth, Tanaka stated in his introduction "I am convinced that [American researchers] will arrive at the realization that violations of international law of the magnitude alleged by Iris Chang in The Rape of Nanking (more than 300,000 murders and 80,000 rapes) never took place."
Chang's book was not published in a translated Japanese language edition until December 2007. Problems with translation efforts surfaced immediately after a contract was signed for the Japanese publishing of the book. A Japanese literary agency informed Chang that several Japanese historians declined to review the translation, and that one professor backed out because of pressure placed on his family from "an unknown organization". According to Japan scholar Ivan P. Hall, revisionist historians in Japan organized a committee of right-wing scholars to condemn the book with repeated appearances at the Foreign Correspondents' Club in Tokyo and throughout Japan. They prevailed on Kashiwa Shobo, the contracted Japanese publisher of the book, to insist that Chang edit the book for "corrections" they wanted made, to delete photographs and alter maps, and to publish a rebuttal to Chang's book. Chang disagreed with the changes and, as a result, withdrew the Japanese publishing of the book. The rebuttal piece was nonetheless published as a book by Nobukatsu Fujioka and Shudo Higashinakano entitled A Study of 'The Rape of Nanking'.
Shudo Higashinakano, a professor of intellectual history at Asia University of Japan, argued in Sankei Shimbun that the book was "pure baloney", that there was "no witness of illegal executions or murders", and that "there existed no 'Rape of Nanking' as alleged by the Tokyo Trial." He identified 90 historical factual errors in the first 64 pages of the book, some of which were corrected in the 1998 Penguin Books edition.
The book was the main source of fame for Iris Chang, who was well respected in China for raising awareness of the Nanking Massacre in the Western world. At the same time, Chang received hate mail, primarily from Japanese ultranationalists, threatening notes on her car and believed her phone was tapped. Her mother said the book "made Iris sad". Suffering from depression, Chang was diagnosed with brief reactive psychosis in August 2004. She began taking medications to stabilize her mood. She wrote:
I can never shake my belief that I was being recruited, and later persecuted, by forces more powerful than I could have imagined. Whether it was the CIA or some other organization I will never know. As long as I am alive, these forces will never stop hounding me.
Succumbing to her battle with depression, Chang took her own life November 9, 2004. A memorial service was held in China by Nanking Massacre survivors coinciding with her funeral in Los Altos California. The Memorial Hall of the Victims in the Nanjing Massacre, a memorial site in Nanjing built to commemorate the victims of the Nanking Massacre, added a wing dedicated to her in 2005.
In the U. S., a Chinese garden in Norfolk, Virginia, which contains a memorial to Minnie Vautrin, added a memorial dedicated to Chang, including her as the latest victim of the Nanking Massacre, and drawing parallels between Chang and Vautrin, who also took her own life. Vautrin exhausted herself trying to protect women and children during the Nanking Massacre and subsequently during the Japanese occupation of Nanjing, finally suffering a nervous breakdown in 1940. She returned to the US for medical treatment, committing suicide a year later.