Did Japanese scientists, like their Nazi counterparts in Europe, use prisoners of war for hideous germ-warfare testing, in violation of the Geneva Convention governing treatment of prisoners?

If they did, the next question is even more appalling: Did the U.S. government agree not to prosecute the war criminals responsible for the experiments in return for the scientific data they had gleaned from their inhumane research?

These two disturbing questions may never be definitively answered. Most of the individuals who could have participated in the alleged atrocities -- both perpetrators and victims -- are dead. Documents that might establish the truth have apparently disappeared.

Our reporter Gary Clouser has been following the limited, unpublicized efforts in Congress to get answers to these haunting questions. Rep. Pat Williams (D-Mont.) has taken the lead in these efforts to determinethe truth. From what he has learned, he believes that both allegations are true: the Japanese government performed biological experiments on American prisoners and the American government covered it up after the war.

As many as 3,000 prisoners of war, including some Americans, allegedly were injected by Japanese scientists in Manchuria with germs that cause the deadliest diseases known: typhus, typhoid, anthrax, cholera, plague, salmonella, tetanus, botulism, smallpox, tuberculosis and encephalitis. In addition, some prisoners were allegedly subjected to freezing conditions to provide information on frostbite.

The accusations first surfaced in the 1950s, and have been the subject of sporadic reports ever since -- including best-selling books in Japan. But the charges have still not been accepted as historical fact.

Congressional attempts to pursue the matter have run into bureaucratic inertia -- and diplomatic reluctance to offend a staunch U.S. ally.

Last year Williams persuaded a House Veterans Affairs subcommittee to hold a hearing, which concentrated on the possibility of giving benefits to the alleged victims. At the hearings, ex-POWs and their relatives testified about the alleged experiments.

In December 1985, Williams held a poorly attended press conference at which he introduced retired Lt. Col. Murray Saunders, a wartime biological warfare expert and aide to Gen. Douglas MacArthur. Saunders said he had been the American negotiator in the immunity deal, and that MacArthur had approved it.

Saunders, who has since died, said it wasn't known at first that human guinea pigs were used in the Japanese experiments, and he acknowledged that he felt ''terrible'' about it in retrospect. But, he added, if the American public had been told the truth immediately after the war, the consequences would have been terrible. ''The war would have to be fought all over again,'' he said.

The American government also had to consider the Cold War, said Saunders. The Soviets, who had heard rumors of the experiments, wanted to interview the Japanese scientists, and the Americans didn't want them to get the militarily useful information.

John H. Hatcher, then the Army's chief archivist, testified at the 1986 House hearing that the Army has no records that would either support or refute the allegations of human experiments or of a cover-up. All the Army had found, he said, was about 200 pages of secondary material captured in Mukden, Manchuria, site of the prison camps where the experiments were allegedly conducted. The documents were highly scientific and hard to translate, Hatcher said, and so were sent back to Japan. Williams termed the Army's failure to translate the material incredible.

Williams first became involved in the controversy seven years ago, when a constituent, Greg Rodriquez, asked for help in getting treatment for maladies he said stemmed from his imprisonment at the Mukden camps. Rodriquez has since died -- as have many of the former POWs.

Williams said he has encountered ''cover-up, denials and an intolerable cloud of secrecy'' during his investigation. Despite diplomatic problems it may cause with Japan, Williams feels that the surviving POWs and their families are entitled to know the truth, ''regardless of the ugliness of it.''

On Oct. 22, surviving American prisoners of war who were held in the Mukden camps will gather for a reunion in Arlington, Texas. Williams hopes to gather more evidence from them.