There has been other threads similar to this in the past, such as: http://www.reddit.com/r/AskHistorians/comments/1rlbx6/during_the_second_sinojapanese_war_was_the_rape/

Basically, the event that became known as the Nanking Massacre was a continuation of brutal treatment of captured Chinese soldiers and civilians that had taken place in the war leading up to that point. Japanese soldiers were encouraged to feel extreme hatred for the Chinese, and the civilians were often regarded as potential spies or partisans.

I will repost my comment from the previous thread:

The "Rape of Nanking" was not a policy ordered from above.

However, as others have commented, officers were not strict in enforcing discipline over their men during the chaos of the battle and its aftermath. Killing, looting, and raping were rampant.

The mass killing of Chinese POW's was also condoned.

I am afraid I don't have much time to write tonight, but here is a copy-paste from an earlier thread about the treatment of POW's and Japanese atrocities:

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Prior to the capture of Nanking, a few incidents of atrocities by Chinese soldiers were widely circulated among the Japanese soldiers.

However, there were some prisoners taken. A Swiss photographer who was in Shanghai in 1937, documented Chinese soldiers brutalizing captured Japanese.

the Chinese soldiers used a variety of torture methods on prisoners, including suspending them in wooden cages by the neck until they died of starvation.

Some were shot, and their bodies stacked for mass burials. Others, mostly Chinese nationals accused of aiding the Japanese, were beheaded with a large sword.

The Tungchow Mutiny took place in 1937 as well. Chinese soldiers who were part of an army loyal to a pro-Japanese collaborator government rebelled when ordered to fight against other Chinese. They quickly overwhelmed the small number of Japanese soldiers and police in the area, and prisoners were not taken.

In addition to Japanese military personnel, some 260 civilians living in Tōngzhōu in accordance with the Boxer Protocol of 1901 were killed in the uprising (predominantly Japanese including the police force and some ethnic Koreans). According to contemporary sources, the majority of women were raped and brutally massacred. Female bodies were found lying on the floor with brooms inserted in their violated genitals; several severed heads of café waitresses were found lining up on a café table in a manner of atrocity exhibition; a woman had her head chopped with a machete, after which the Chinese perpetrator raped the body in a necrophilic act; the intestines was savagely taken out of the body; a child was found dead with a barbed wire nose ring pierced in the nostrils. Only around 60 Japanese civilians survived and they provided both journalists and later historians with firsthand witness accounts. To complete their orgy, the Chinese set fire and destroyed much of the city.

The atrocities committed during the mutiny were used by the Japanese government to motivate soldiers to "暴戻支那膺懲" (punish atrocious China).

That "punishment" would prove far more atrocious than the initial atrocities against Japanese. Throughout the war, Japanese would kill Chinese who surrendered. It was especially terrible after the capture of Nanking, when thousands of Chinese prisoners were lined up and shot.