Only the winners decide what were war crimes.
Gary Wills
Unit 731
Unit 731 was a center (the largest of several) for intensive chemical-biological warfare testing located in China during the Second World War and run by the Japanese. Not only was it engaged in testing the weapons but tested them on human beings (Chinese civilians and Russian, Korean, and allied prisoners of war), including medical experiments, dissections, vivisections, and some things done without even the pretense of being potentially beneficial for the war effort.
It is unclear just how many died there but estimates are at least 3000 between 1940 and the end of the war and possibly as many as 9000 total (nowhere near concentration camp numbers from the European Theater, but experimentation far exceeded anything the Nazis dreamed up). Thousands of others perished as a result of the work there. Some who had helped build the "camp" as forced labor (many of whom became the first group of guinea pigs), and many innocent civilians who were bombed with various biological and chemical agents by the Japanese were also casualties of the program. Further, the leftover and buried weapons became a health and environmental hazard for years after. When the unit was shut down, it also released thousands of plague-bearing rats that had been bred there. It took three months to control the outbreak, leaving as many as 20,000 dead.
One of the blackest moments in the history of the twentieth century (which certainly has its share), the story of Unit 731 is made still worse by the way those responsible escaped justice and returned to society without penalty, in some cases becoming prominent members of the medical community. The chief reason this was made possible was that they were helped by the United States in exchange for information.
What was known
The US government (at least the military) was well aware that Japan had and was willing to use chemical/biological weapons. In August 1937, Japan used poison gas against Chinese soldiers. This practice was not isolated, as gas was used well over one thousand times during the course of the war, as well as various biological weapons, usually plague. The US was also aware of the research going on and Unit 731, itself.
That it was known and nothing done should not be too surprising as things outside the immediate scope of the US and its immediate objectives were often overlooked or devalued. This was not uncommon and can be demonstrated by the knowledge of Hitler's extermination camps and the Rape of Nanking (granted, in none of the cases was the extent of the atrocities and many of the details known, but the US—and other Western nations—were far from being in the dark that these things were going on).
One of the reasons the US is thought to have not been concerned with the development of the weapons is because of the distance involved. There was little belief that Japan could launch a successful attack on the US from way over there (that all sides refrained from use in the European Theater may also have reinforced this belief—later). There is also a suggestion that it was partially racially motivated, as the West didn't believe the Japanese were capable of producing and utilizing something so deadly. (A certain degree of racism, along with the distance, may have led to ignoring the atrocities being committed to the yellow Chinese.)
In 1942, an article appeared in the Rocky Mountain Medical Journal that was titled "Japanese Use the Chinese as 'Guinea Pigs' to Test Germ Warfare." It seems hardly plausible that (even if—a hypothetical if—they didn't already know) a nation in the midst of a World War would allow something like that to slip under the radar of intelligence. As more Japanese were captured, the extent of the program was revealed and it was far larger than the US had assumed. Knowledge of the location and its purpose was known as well as its size and the bombs (for the purpose of spreading biological agents) being made there. They were also aware that Ishii Shiro was the head of the whole thing.
In 1943, the US began its own program of perfecting and manufacturing biological weapons. It grew quickly and the program was quite successful. On the other hand, the US had started well behind other nations in the research and development—therein lies the motive.
Hunting down the "Doctors"
Within a week of the surrender, Lieutenant Colonel Murry Sanders (who headed the US program), was in Japan with others looking for the people who had been involved in the Japanese chemical/biological warfare effort (emphasis on the biological component). Ishii in particular.
Many of the men involved were found and interviewed (Ishii couldn't be found at the time). The man assigned as an interpreter had been former student of Ishii's and probably misled the investigation. In order to speed along the process and to make the "doctors" more willing to cooperate and part with information, Sanders decided to grant them immunity from prosecution. He suggested to General Douglas MacArthur that "we promise Naito [the interpreter] that no one involved in BW [biological weapons] will be prosecuted as a war criminal" (www-users.cs.umn.edu). MacArthur agreed.
Sanders did uncover the truth about the human experimentation. When informed, MacArthur's response was that "we need more evidence. We can't simply act on that. Keep going. Ask more questions. And keep quiet about it" (www-users.cs.umn.edu). Of course, no action was taken and silence was all but assured.
International Military Tribunal for the Far East
After ten weeks, Sanders returned to the US. Before he left he informed his successor in the "investigation," Lieutenant Colonel Avro Thompson, of the human experiments and the development of the biological bombs.
Ishii finally turned up. He had remained hidden by having a sham funeral staged in his hometown and the papers went along with it. Thompson interrogated him for about five weeks between January and February 1946. Ishii was very careful not to admit too much and described the program as much smaller than it was and did not implicate Emperor Hirohito for his involvement. He also denied human experimentation. Yet he did brag about his great knowledge on the subject and gave information on the production of germs and germ bombs. Information gladly accepted and assimilated by the US.
When the International Military Tribunal for the Far East began trying Japanese war criminals in 1946 (which took over two years, far longer than the Nuremberg trials), it would seem that the men who ran Unit 731 would be prime candidates for sentencing, given the knowledge and evidence from China that had been recently gathered. This was not to be.
In May 1947, MacArthur (this was also the desire of many or most of the scientists working on the US program and other military personnel) sent a radio message back to Washington, D.C. in reference to the immunity:
Ishii states that if guaranteed immunity from "war crimes" in documentary form for himself, superiors and subordinates, he can describe program in detail.... Complete story, to include plans and theories of Ishii and superiors, probably can be obtained by document immunity to Ishii and associates.
A few months later when the Committee for the Far East subcommittee for the State-War-Navy Coordinating Committee issued its report on his recommendation, it pointed out that similar experiments perpetrated by the Nazis had been condemned and punished as war crimes in the Nuremberg trials. At the same time, it agreed, stating that "the value to the US of Japanese BW data is of such importance to national security as to far outweigh the value accruing from war crimes' prosecution."
The State Department felt it was unwise and would cause severe embarrassment if it was revealed what happened. The Committee went ahead and okayed the recommendation, saying that any information "should be retained in 'top secret' intelligence channels and not employed as war crimes evidence." Additional concerns were that the Soviet Union would get hold of the information for its own use (the Soviets tried supplying evidence for the atrocities to be used at trial but it was refused; they later held their own, see below). It March 1948, the Joint Chiefs of Staff gave their official approval. Nine months later the trial was over.
Only once did the topic of biological weapons even come up 29 August 1946—which demonstrates that not only was an "official" course of action unnecessary to be approved, but that there was little or no intention on the part of the prosecutors to investigate that subject. The assistant US prosecutor brought it up by saying that
The enemy's Tama Detachment carried off their civilian captives to the medical laboratory, where the reactions to poisonous serums were tested. This detachment was one of the most secret organizations. The number of persons slaughtered by this detachment cannot be ascertained
When asked if he was to present any evidence, he replied "we do not at this time anticipate introducing additional evidence on that subject" (pw1.netcom.com). The US defense attorneys argued that there was no sufficient evidence to continue that line and that it could have been vaccinations for health purposes. It was dropped (without protest) for the entirety of the trial.
Not that it would have had an effect on those in Unit 731, as it was directly related to the Nanking unit. It's not implausible that even if it had been pursued, Ishii and his other personnel would have been ignored.
But knowledge of the experiments had already begun to be spread. On 6 January 1946 (over seven months before that day in court), the Pacific Stars and Stripes—which is published by the army—mentioned that Americans had been victims of the experiments. Within a week it had appeared in the New York Times. Again, for the military to "miss" not only one of its own official newspapers but the US "paper of record," makes the claim that no evidence exists or the idea that the subject is not worthy of additional investigation ring hollow.
In a government document from August 1947 it was noted that
It should be kept in mind that there is a remote possibility that independent investigation conducted by the Soviets in the Mukden area may have disclosed evidence that American prisoners of war were used for experimental purposes of a BW nature and that they lost their lives as a result of these experiments
The US knew what happened, where, and by whom. And these crimes were swept under a rock, leaving the perpetrators to go on with their lives, all in the name of "national security." Or as 1947 memo that shows the investigation was under the order of the Joint Chiefs of Staff put it, "every step, interrogation, or contact must be coordinated with this section... The utmost secrecy is essential in order to protect the interests of the United States and to guard against embarrassment" (wansui.huaren.org).
As late as 1995, the deputy information director at the Pentagon stated "nobody has ever come up with solid evidence. But that doesn't mean we're not interested in seeing it" (wansui.huaren.org). Indeed.
Soviet trial
After the war (1949), Russia tried twelve members of the unit for war crimes. One got only two years imprisonment, another three, and the rest got between twenty and twenty-five years. Except for one who committed suicide, they all lived until they were released and repatriated to Japan in 1956. Some charge that the leniency of the sentences contrasted with the level of the crimes was due to a deal made for information on the weapons. This, of course, would be seen as "proof" of the evil and corruption of the Soviet Union from the American point of view. But for the US, its deal was perfectly reasonable. In the US, the trial was discredited as being nothing but a "show trial" and indicative of the sort of propaganda stunts Joseph Stalin was known to try.
"Doctors" post-war
With immunity intact, there was little for the former personnel of the unit(s) to be concerned with. With the exception of the twelve tried by the Soviet Union—who spent only a short time incarcerated before returning—the only one who had any obstacles was Ishii, himself, who was barred from being appointed to any important posts after the war. He died in 1959 at the age of 69.
The rest were free to enter the private or public sector as they chose. And did. Among the many prestigious and lucrative positions held by former unit officials were presidents, vice presidents, directors, and professors of universities and colleges—often medical colleges or the medical schools within universities. Some worked for the National Institute for Health, pharmaceutical companies, and private medical practices. The man who had been Sanders' interpreter went on to establish the Japan Blood Bank Company along with others from the unit. Another became secretary for the Japanese Penicillin Association. Some became part of the Ministry of Health and the Japan Medical Association.
Along with the US immunity (which also protected them from public denunciation), the Japanese institutional tendency to deny atrocities that took place during the war aided the men. Much like the Rape of Nanking, any mention of Unit 731 and its satellite units was absent from the history books. And given the original secrecy surrounding the project, it was even more censored. It wasn't until things started leaking out in the latter decades of the twentieth century, that citizens became aware of what happened, even as rumor or assertion.
A series of lawsuits was filed, one pertaining to Unit 731. It wasn't until August 1998 that the Supreme Court ruled that the "existence of the unit was accepted in academic circles" (shenware.virtualave.net). The silence hardly ended there. In the 5 June 2001 online edition of the Japan Times, an article notes that "even as war-crimes victims and their descendants are suing the Japanese government for compensation, the nation's Education Ministry approved a textbook this past April glossing over the Imperial Japanese Army's wartime culpability" (www.japantimes.co.jp). The government has yet to offer reparations or a sincere and adequate apology for its actions.
Conclusion
Meanwhile in the US, claims by former prisoners of war who suffered for years from maladies that they were certain came from their time with the units were mostly ignored. In 1996, a House Resolution was introduced that demands Japan give up all information on wartime atrocities, particularly Unit 731, apologize, and begin paying reparations to the victims. In 1998, another version—more broad in scope—was introduced. (As far as I know this has yet to be passed.)
About the only penalty "suffered" by those involved has been the Department of Justice listing of sixteen Japanese men as war criminals (only some of whom were part of the unit, the others were for other reasons), making them unable to set foot on American soil. Calls for reparations have also been denied or ignored. Other possible Japanese war criminals might also be barred entrance but the Japanese government is "reluctant" to turn over Imperial Army records.
Perhaps one of bitterest ironies of the whole thing is that it actually did little for the US biological weapons program. It turned out that the US program had advanced far enough along that the Japanese information was not as valuable as it purported or was assumed to be. The criminals escaped punishment and victims continued to suffer.
(Sources: www-users.cs.umn.edu/~dyue/wiihist/germwar/731rev.htm quotes from here unless noted, www-users.cs.umn.edu/~dyue/wiihist/germwar/germwar.htm, www.sjwar.org/731/731.htm, shenware.virtualave.net/his_unit731.shtml, www.vcn.bc.ca/alpha/speech/Harris.htm, www.japantimes.co.jp/cgi-bin/getarticle.pl5?eo20010605a1.htm, pw1.netcom.com/~aguldo/agga/bt/txt/bt081946.htm, wansui.huaren.org/~aohwa/2001/pow199~1.htm)