There is some debate as to the extent of the war atrocities in Nanjing, especially estimations of the death toll.

The issues involved in calculating the number of dead lie in defining the geographical range and time period of killing as well as the question of what "type" of killing is to be included in the definition of the term "massacre". On one side is the view that the geographical area of the incident should be limited to the few square kilometers of the city known as the Safety Zone. Another view to define "Nanjing" as the old walled city of Nanjing. Some historians include a much larger area around the city. The Xianquan area is the suburbs of Nanjing city (which is about 66 miles). Because the entire Jiangsu province fell under the administration of Nanjing, some historians also include six xian (counties) around Nanjing starting from Suzhou, at the western edge of Jiangsu province.

The period of the massacre, hence, is naturally defined by the geography of the massacre. The Battle of Nanjing ended on December 13, when the divisions of the Japanese Army entered the walled city of Nanjing. The Tokyo War Crime Tribunal then defined the period of the massacre to the ensuing 6 weeks. Conservative estimates say the massacre started from December 14th, when the troops entered the Safety Zone, and that it lasted for 6 weeks. Those who define the Nanjing massacre as having started from the time the Japanese army entered Jiangsu province push the beginning of the massacre to around mid-November to early December (Suzhou fell on November 19), and stretch the end of the massacre to late March 1938.

Another point of debate is the question of whom to count as the victims of Japanese atrocities. Historians agree that the Japanese army indiscriminately killed many civilians in Nanjing city, and that these should be counted in the death toll of the massacre. Over the course of the campaign through China, the Japanese army did not take prisoners of war and summarily executed Chinese soldiers during or after combat. Moreover, the army executed plain-clothed guerilla combatants who were hiding among civilians. It is unclear how many innocent civilians were wrongly accused of being guerilla combatants and were dispatched in this manner.

To make matters more difficult, archival evidence such as burial records only state the body count and not which type of group to which each body belonged. Therefore, it provides no means to distinguish whether bodies were the result of "legitimate" or "illegitimate" killing. Many different categories of varying legitimacy exist: soldiers killed during combat, surrendered soldiers summarily executed after the battle, plain-clothed guerilla combatants, plain-clothed soldiers hiding among civilians, civilians wrongly suspected of being guerrila combatants, or those bystanders attacked during the period of indiscriminate killing, rape and looting (which all the scholars deem to be illegitimate).

In the International Military Tribunal for the Far East or the Nanjing War Crimes Tribunal, death toll is given to range between 200,000 and 300,000. The death toll reckoned at the Nanjing War Crimes Tribunal, is the official estimate engraved on the stone wall at the entrance of the "Memorial Hall for Compatriot Victims of the Japanese Military's Nanjing Massacre".

In 1947 at the Nanjing War Crimes Tribunal, the verdict of Lieutenant General Tani Hisao, the commander of the 6th Division, quoted the figure of more than 300,000 death tolls. Apparently the estimation was made from burial records and eyewitness accounts. It concluded that some 190,000 were illegally executed at various execution sites and 150,000 were individually massacred. The International Military Tribunal for the Far East estimated in its judgment that "over 200,000" or "over 100,000" civilians and prisoners of war were murdered during the first six weeks of the Japanese occupation. That number was based on burial records submitted by two charitable organizations, the Red Swastika Society and the Chung Shan Tang (Tsung Shan Tong), the research done by Smythe and some estimates given by survivors.

At the Tokyo Tribunal of War Criminals, the Nanjing Massacre death toll was presented either as "more than 200,000" or "more than 100,000". The extent of Japanese atrocities shocked the world as well as the Japanese public of the time.