He was born in Kumamoto prefecture, Japan, in 1916. In 1938, he was dispatched to Wujiang county, Jiangsu province, in China as a member of the propaganda branch of Japan's Central China Expeditionary Army. After Japan's surrender in August 1945, he took refuge among the troops of Yan Xishan, a military officer of the Kuomintang. He was captured and taken into custody in Shanxi in 1949 and arrested on Dec 9, 1950.

During his service in the Japanese army, with the Yan Xishan troops and in the war of liberation, he committed a number of crimes, including fatally shooting 88 Chinese residents; stabbing nine to death; burying two people alive; burning 26; drowning one; dropping six to their deaths from a height; and killing 41 with a Japanese sword or straw cutter.

Nagatomi killed 61 Chinese soldiers from the Central Army, South Shanxi Field Army and Anti-Japanese Army.

From the start of Japan's invasion of China to Japan's surrender, Nagatomi personally killed 61 Chinese people, ordered the killing of 166 and ordered the killing of 41 people under a superior order.

In court cases, he was found to have raped five married women and two unmarried girls. He established a so-called "comfort" station, where Japanese soldiers committed sexual crimes involving 12 women. He later confessed to personally raping 18 Chinese women.

In April 1938, as a demonstration to generals and other officers, he beheaded a captive with a sword in Wujiang county and raped a Chinese woman.

In November 1942, during a cleanup operation in Wenxi county, he arrested three soldiers of the South Shanxi Field Army and beheaded them beside a well in Hengshui township to test whether a Japanese sword made by a Chinese blacksmith was effective. He pushed six Chinese residents off a cliff to kill them, and drove 20 Chinese women and children to a cave in the Taiyue Mountains and burned them alive.

In July 1944, Nagatomi set up a comfort station to indulge Security Team members, as well as to satisfy his own lust while serving as the instructor of the Security Team in Huoxian county.

In December 1944, Nagatomi arrested three villagers and interrogated them with torture in Lijiashan, Huoxian county. Failing to get any information, he ordered soldiers to kill them all. He killed 11 people with a rifle south of Xixu village.