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This answer was posted in response to the original question:
I am seeking information on the locating and detaining of suspected Nazi war criminals and SS officials near and shortly after the end of WWII in Europe. Specifically, was there an organized or coordinated effort charged with this task similar to the effort to locate and return stolen art by the officers and men of the Monuments, Fine Arts, and Archives (MFAA) program? If so, how was this unit(s) organized, what were their standing orders, when were they commissioned and decommissioned for this task, and who commanded the unit(s)?
It does not deal with the question of gathering evidence of War Crimes, Crimes Against Peace, Crimes Against Humanity etc. which seems to be the focus of the update to the question.
Those investigations would have been carried out under the rules set out in Section III of the Charter for the International Military Tribunal: Committee for the Investigation and Prosecution of Major War Criminals.
No specialist units were created to locate and detain suspected Nazi war criminals and SS officials.
However, the Directive to the Commander in Chief of the U.S. Occupation Forces (JCS 1067) in April 1945 (which would be the basic directive regarding military government in Germany) stated simply:
- Suspected War Criminals and Security Arrests:
a. You will search out, arrest, and hold, pending receipt by you of further instructions as to their disposition, Adolf Hitler, his chief Nazi associates, other war criminals and all persons who have participated in planning or carrying out Nazi enterprises involving or resulting in atrocities or war crimes.
It was thus the responsibility of all allied military personnel to identify, arrest and detain suspected war criminals.
The development of allied policy, from the Moscow Declaration by the United Kingdom, the United States, and the Soviet Union, “Declaration on German Atrocities in Occupied Europe” in November 1943, through to the Nuremberg trials is discussed in some detail in a 2011 doctoral thesis by K.J. Heller titled The Nuremberg Military Tribunals and the origins of International Criminal Law.
The introductory chapter of that thesis, From the IMT to the Zonal Trials, probably contains the information you're seeking.