Part 1

As a – at least for me when I first read about it – turn of what seems like putting the fox in charge of the henhouse, there indeed was an official Wehrmacht War Crimes Bureau (Wehrmacht Untersuchungsstelle fur Verletzungen des Volkerrechts) established with the outbreak of the war in 1939 and charged with investigating both violations of international law committed by civilians and members of foreign armed forces against German personnel as well as investigating any such accusations leveled against German Wehrmacht forces by foreign countries.

It's important to preface this by saying that despite numerous mentions in various pieces of historical fiction (most notably, Philip Kerr's Bernie Gunther novels), there only exists one serious work of scholarship about the Bureau, The Wehrmacht War Crimes Bureau, 1939-1945 written by Alfred-Maurice de Zayas, Cuban-American historian and noted human rights lawyer and since 2012 UN Independent Expert on the Promotion of a Democratic and Equitable International Order. Aside de Zayas being a rather unusual source for a rather unusual book, he himself notes that it is really difficult to research the history and practice of the Wehrmacht War Crimes Bureau since most of their files were destroyed before the end of the war. De Zayas notes that of the about 10.000 cases they investigated in their six year history, only 4000 remain and his scholarship is mostly based on these. It is notable that a lot of the destroyed files seem to have dealt with cases concerning war crimes that occurred in the Soviet Union and it is unknown if these contained investigations on German personnel though in light of the so-called Barbarossa Decree, which stated that no German soldier could be prosecuted for war crimes committed in the war against the USSR, this seems unlikely.

But on the how, why, and what: In general, every modern military has legal experts whose primary responsibility is to administer military justice, maintain discipline, and monitor the observance of the laws and customs of war (in the US this would be the Judge Advocate General Corps e.g.) and Germany was no exception. On 4 September 1939 then General (later Field Marshal) Wilhelm Keitel issued a decree founding the the Wehrmacht Untersuchungsstelle fur Verletzungen des Volkerrechts with the assigned the task "to ascertain violations of international law committed by enemy military and civilian persons against members of the German armed forces, and at the same time to investigate whatever accusations foreign countries should make against the Wehrmacht". The basic idea behind this was that this bureau, staffed with judges, was to monitor and investigate compliance with the Hague and Geneva conventions by states and armed forces participating in the war. It's chief was Johannes Goldsche, former deputy chief of the institutional equivalent of the bureau in the German Army of WWI.

Right here at the start, however, one caveat was made clear that exemplifies a crucial difference between the Wehrmacht bureau and its equivalent in the US; GB, France and elsewhere: Unlike their bureaus who investigated both German war crimes and allegations against soldiers of their own army, the Wehrmacht bureau was indeed only able to investigate the Wehrmacht. The bureau was not competent to investigate violations of the laws of war perpetrated by Himmler's SS, which became immediately relevant. As /u/kieslowskifan describes in their answer here, the Poland campaign create frictions between the SS and the Wehrmacht because, among other things, their criminal conduct in Poland. While this was gone by the time the attack on the USSR rolled around, the Wehrmacht bureau could not be brought to bear as a pressure tool against the SS in 1939 in connection to the Poland campaign.

And even if they could have investigated, how reliable would an investigation by the Wehrmacht War Crimes Bureau be? Germany was notorious for staging incidents such as the Gleiwitz incident to justify starting a war as well as massively over-exaggerating incidents such as the Nemmersdorf massacre for propagandistic use, so when we look at the files of the bureau, we need to immediately try to asses how reliable they are.

De Zayas tries to do exactly that in his work. He writes:

I was able to interview the two survivors and to locate the personnel files of the other members at the Bundesarchiv-Kornelimuinster and at the Wehrmacht-Auskunftstelle in Berlin, and further to obtain valuable information and photographs from their relatives. It became clear that none of them was a Nazi activist or fanatic like Roland Freisler, the president of the People's Court. On the contrary, it became apparent that the bureau members had been working in an environment where many opponents of national socialism had come together. (...)

A careful study of the records followed - not only of the 226 volumes, but also of the relevant files of other German offices with which the bureau had regular contacts. These were, inter alia, the Amt Ausland-Abwehr, the Wehrmachtfuihrungsstab, the Army Medical Office (Heeressanitätsinspekteur) and the Auswartiges Amt. Nowhere was there evidence of any doctoring of documents or of fabrication. There were no guidelines from the Propaganda ministry, no interference from Hitler, Himmler, Goebbels, Heydrich, Kaltenbrunner. The members of the bureau were essentially left alone to carry out their assignment, which they did without fanfare. It is interesting to note that there are no comments in the internal correspondence that would indicate adherence to Nazi ideology, no anti-semitic observations, no jaded remarks. What becomes obvious from the study of the unfortunately incomplete internal correspondence is that bureau members had a subjective conviction that the Allies, in the first place the Soviets, were grossly violating international law.

It's an interesting assessment and de Zayas cites an internal memo from Goldsche insisting on cataloguing Allied war crimes in order to combat what he calls "Allied propaganda" after the war was over and thus disqualify the charges levelled at the Germans and the Wehrmacht. This is interesting in as far, and de Zayas notes his awareness of that, that given how crucial the German army was to to the criminal conduct of the Nazi state, how it encouraged terror as a form of warfare and made atrocities part of its officila policy and how widespread knowledge of these atrocities was – though the latter part was most likely unknown to de Zayas when he wrote his book in 1979 due to the fact that this is a result of recent research –, this begins to cast some doubt on the investigators and politics of the Bureau.

I mean, he cites the head of the bureau with:

Our enemies in the world war earnestly endeavoured to collect our alleged wartime misdeeds, classify them, and make an indictment out of them so as to brand the Germans as outlaws for all time and thus to disqualify them in the arena of world politics. Because of their inexhaustible propaganda methods, their concerted pressure, and the weakened stance of postwar German governments, they were largely successful. There is no doubt that upon the conclusion of peace after this war, this disgrace ought to be wiped out. One of the means to this end, which the Wehrmacht should provide for, is the preparation of a catalogue of war crimes and crimes against humanity perpetrated by our enemies on land, sea and in the air

which was written in 1942 at a point when the Wehrmacht had assisted the Einsatzgruppen killing almost half a million people; had killed the male Jews of Serbia together with about 20.000 other Serb civilians; and had starved about one and a half million Soviet POWs to death – facts Goldsche and his colleagues were most likely aware of in some sort or form. To, at this point, talk of propaganda when it comes to Allied allegations of criminal conduct speaks of a serious disconnect. And while the members of the Bureau might not have been dyed in the wool Nazis, they still practiced that peculiar disconnect of not seeing or not wanting to see that there were indeed war crimes committed by the Wehrmacht and the German state.

But on to their modus operandi, meaning how did they investigate war crimes. Usually, the members of the Bureau itself as well as deputized civilian and military judges did indeed conduct serious investigations into allegations they heard, e.g. 44 of them traveled to Poland to interview witnesses and victims of crimes committed against German soldiers and German or Volksdeutsche civilians; assess reports; and come to a full version of events. De Zayas points out in his assessment that their modus operandi was functionally sound: They dismissed hearsay (such as when they investigated charges that Allies had shot on German parachutists while they were still in the air during the invasion of Crete), they tried to obtain as much confirmation as possible and at least the surviving records show that serious investigations were conducted, intended to show what happened indeed instead of just feeding the Nazi propaganda machine.