NAGO, Japan— Shortly before the end of World War II, just after the United States won the brutal battle for Okinawa, three American marines stationed in this sun-drenched archipelago disappeared.

At first, the Marine Corps listed the three, all 19 years old and black, as possible deserters in the summer of 1945. A year later, when there was still no trace of them, they were declared missing in action.

For five decades, the case was forgotten. Then in 1998, the local police, acting on a tip, discovered what proved to be the bones of the three marines in a cave just north of this resort town. After long examinations, the remains were sent to relatives in the United States for burial early this year.

But the discovery did little to solve the mystery of the marines' disappearance and, far from putting the case to rest, dredged up powerful local resentment about how Americans treated Okinawans after the fighting stopped.

Some elderly Okinawans, who grew up near where the remains were found, are now willing to tell a long-held secret: a group of villagers ambushed and killed the three men, thinking they were the three black marines who the villagers believed had repeatedly come to the village to rape the village women.

While much of what the Okinawans said about those painful days after the war ended is corroborated, it has not been proved that these three marines committed any rape. Nor has it been confirmed that the villagers in fact killed the soldiers, although there is strong evidence that they did.

Still, the villagers' tale of a dark, long-kept secret has refocused attention on what historians say is one of the most widely ignored crimes of the war, the widespread rape of Okinawan women by American servicemen.

Much has been written and debated about atrocities that Okinawans suffered at the hands of both the Americans and Japanese in one of the deadliest battles of the war. More than 200,000 soldiers and civilians, including one-third of the population of Okinawa, were killed.

There has been scant mention of rape afterward. But by one academic's estimate, as many as 10,000 Okinawan women may have been raped and rape was so prevalent that most Okinawans over age 65 either know or have heard of a woman who was raped in the aftermath of the war.

''I have read many accounts of such rapes in Okinawan newspapers and books, but few people know about them or are willing to talk about them,'' said Steve Rabson, a professor of East Asian Studies at Brown University, who is an expert on Okinawa.

Marine Corps officials in Okinawa and Washington said that they knew of no rapes by American servicemen in Okinawa at the end of the war, and their records do not list war crimes committed by marines in Okinawa.

Gen. John G. Castellaw, deputy commander of the Marine force in Okinawa, said that during the past 30 years, in which he completed numerous assignments on the island, he had never heard of any accusations of widespread rape by American servicemen in Okinawa.

The New York Times tried to contact surviving members of the segregated 37th Marine Depot Unit, to which the three dead marines were attached. But the Montford Point Marine Association, a veterans group representing the marines who were trained at Montford Point, N.C., said it could not locate any veterans willing to be interviewed.

Samuel Saxton, a retired captain who is the association's immediate past president, said in a telephone interview that it was important to learn the truth about the marines' deaths and whether Americans committed rapes in Okinawa. But he said he feared that black marines who served there, and made up only a part of the Americans stationed on Okinawa, would be wrongly painted with a broad brush.

''It would be unfair for the public to get the impression that we were all a bunch of rapists after we worked so hard to serve our country,'' he said.

Books, diaries, articles and other documents refer to rapes by American soldiers of various races and backgrounds.

Masaie Ishihara, a sociology professor at the Okinawa International University, said ''there is a lot of historical amnesia out there'' about those traumatic postwar years. He said that ''many people don't want to acknowledge what really happened.''

One possible explanation for why the United States military says it has no record of any rapes is that few if any Okinawan women reported being attacked out of fear and embarrassment, and that those who did were ignored by the United States military police, the historians said. Moreover, there has never been a large-scale effort to determine the real extent of such crimes.

Even today, efforts to speak to women who had been raped were rejected because friends, local historians and university professors who had spoken with the women said they preferred not to discuss it publicly.

''Victimized women feel too ashamed to make it public, and criminals who killed the three marines are afraid,'' said a police spokesman in the nearby city of Nago.

In his book ''Tennozan: The Battle of Okinawa and the Atomic Bomb,'' (Ticknor & Fields, 1992) George Feifer said that there were fewer than 10 reported cases of rape by 1946 in Okinawa, ''partly because of shame and disgrace, partly because Americans were victors and occupiers.'' Mr. Feifer said that ''in all there were probably thousands of incidents, but the victims' silence kept rape another dirty secret of the campaign.''