The Manila massacre was one of several major war crimes committed by the Imperial Japanese Army, as judged by the postwar military tribunal.

The Japanese commanding general, Tomoyuki Yamashita, and his chief of staff Akira Mutō, were held responsible for the massacre and other war crimes in a trial which started in October 1945.

[1]: 113 Dr. Antonio Gisbert told of the murder of his father and brother at the Palacio del Gobernador, saying, "I am one of those few survivors, not more than 50 in all out of more than 3000 men herded into Fort Santiago and, two days later, massacred.

[4] The Japanese conducted mop-up operations to clear north Manila of guerrillas, executing more than 54,000 Filipinos, including children, as they passed through towns.

[10][11][2] Some historians, citing a higher civilian casualty rate for the entire battle, suggest that 100,000 to 500,000 died as a result of the Manila massacre on its own, exclusive of other causes.

Former war-crimes prosecutor and author Allan Ryan argues that there was no evidence that Yamashita committed crimes there, ordered others to do so, was in a position to prevent them, or even suspected they were about to happen.

[citation needed] However, the problem with this argument was that Yamashita's lawyers resorted to using a chain of command technicality defense related to how the Japanese Navy were solely responsible for the massacre in Manila as a way to excuse Yamashita of committing all war crimes in the Philippines, of which there were many outside of Manila, according to the Chief of the Government Section for the Supreme Commander for the Allied Powers and Chief of Civil Affairs Section, U.S. Army Forces, Pacific Ocean Area, Brigadier General Courtney Whitney.

It was argued that Yamashita was in full command of the Japanese Army's secret military police, the Kempeitai, which committed numerous war crimes on POWs and civilian internees and he simply nodded his head without protest when asked by his Kempeitai subordinates to execute people without due process or trials because there were too many prisoners to do proper trials.

Philippine Army generals Lim, Simeon de Jesus, and Fidel Segundo were beheaded alongside hundreds of other people in mass graves by Army soldiers in Manila without a trial or due process on Yamashita's orders, long before Yamashita left Manila.

The Japanese Navy and Rear Admiral Sanji Iwabuchi had nothing to do with the massacres done by Yamashita's Kempeitai and regular Army soldiers that were under his chain of command.