Yamashita's culpability for these events remains a matter of controversy, as some argued that he had failed to prevent them.However, Yamashita had the officer who instigated the hospital massacre, and some soldiers caught looting, executed for these acts, and he personally apologized to the surviving Alexandra Hospital patients.Despite his ability, Yamashita fell into disfavor as a result of his involvement with political factions within the Japanese military. After the February 26 Incident of 1936, he fell into disfavor with Emperor Hirohito due to his appeal for leniency toward rebel officers involved in the attempted coup.As a leading member of the "Imperial Way" group, he became a rival to Hideki Tōjō and other members of the "Control Faction". Yamashita was given command of the elite 3rd Imperial Infantry Regiment. He realized that he had lost the trust of the Emperor and decided to resign from the Army--a decision that his superiors dissuaded him from carrying out.Yamashita remarked that only a "driving charge" would ensure victory in Malaya.This is because the Japanese force was about one-third of what the British had in Malaya and Singapore.
Akashi Yoji argued in his article "General Yamashita Tomoyuki: Commander of the Twenty-Fifth Army" that his time in Korea gave him the chance to reflect on his conduct during the 1936 coup and at the same time study Zen Buddhism, something which caused him to mellow down in character yet instilled a high level of discipline for himself.
He attended military preparatory schools in his youth. He twice served in the Military Affairs Bureau of the War Ministry responsible for the Ugaki Army Reduction Program, which was aimed at reforming the Japanese army by streamlining its organisation, despite facing fierce opposition from factions within the Army itself. Yamashita served in the Imperial Headquarters and the Staff College, receiving promotion to lieutenant-colonel in August 1925.
In November 1905 Yamashita graduated from the 18th class of the Imperial Japanese Army Academy. While posted to the Imperial Japanese Army General Staff, Yamashita unsuccessfully promoted a military reduction plan.
In a controversial trial, Yamashita was found guilty of his troops' atrocities even though there was no evidence that he approved or even knew of them, and indeed many of the atrocities were committed by troops not actually under Yamashita's command.
This ruling – holding the commander responsible for his or her subordinates' war crimes as long as the commander did not attempt to discover and stop them from occurring – came to be known as the Yamashita standard.
While he was unable to stop the US advance, he was able to hold on to part of Luzon until after the formal Japanese surrender in August 1945.