Even more complicated than that...the naval commander of Manila had been disgraced for losing his command (the battleship Kirishima) in the Solomons/Gilberts area, and his land assignment was a permanent punishment. He chose to hold the city when Yamashita withdrew, and since there was no concept of joint command in the Japanese military (the Army and Navy were more rivals than peers) Yamashita couldn’t order the naval garrison of Manila (who committed the bulk of the atrocities) to do a thing.
And yet, after the war Yamashita was effectively hanged for something over which he had no control.
“Yamashita was effectively hanged for something over which he had no control.”
The author of the book is of the opinion that Yamashita almost certainly knew what they were doing while it was underway (they had ongoing communications), and that he was likely complicit in the decision to delay in the city and to kill the civilians - and it is a good chance that High Command in Tokyo was equally well informed and complicit. The orders may well have come from Tokyo, perhaps with knowledge of the Emperor.
It was more a case that the high standard of evidence of an American Capital Punishment case could not be clearly met (radio communications had not been recorded, no damning written communications had been captured intact).
The local commander in the City (Sanji Iwabuchi) was willing to dutifully and knowingly take the responsibility to the grave with him like a good soldier, just as he was willing to ritually take his own life right on cue. The American Military Authorities were not going to let this monster (Yamashita) off because of technicalities of our legal system.
The Americans knew that the Japanese chain of command was intact, that they were in regular communication, and that Iwabuni dutifully obeyed orders in every other respect. They just didn’t have rock solid documentation of a direct order, and defense counsel advised Yamashita that he would be executed if he confessed to it.
Of the 15 to 20 thousand Japanese forces in the city, virtually all of them were willing to obey to the death. Only about a hundred survived, mostly captured wounded and unable to kill themselves, or unconscious.