The incident has become public when president-elect Bill Clinton is under pressure from gay groups to proceed quickly with his plans, opposed by his generals, to abolish the Pentagon's longstanding prohibition on homosexuals.
Although the motive is unclear, navy officials have confirmed to the Los Angeles Times newspaper that the sailor, Allen Schindler, a 22-year-old radioman from Chicago, may have been the victim of a gay-bashing attack.
The incident happened in October at a public convenience near the US naval base at Sasebo, Japan, where Schindler's ship, the Belleau Wood, was based. The military has been sparing with details, but family members have reportedly said that he was beaten beyond recognition, and identifiable only by his tattooed forearms.
His mother has also claimed that his penis was lacerated in the attack, a detail which appears to support the theory that he died in a hate crime. Schindler was being processed for an administrative discharge as an acknowledged homosexual. A 20-year-old airman has been arrested and charged in connection with the killing.
Schindler's appalling death can be used as evidence by either side of the deeply acrimonious debate over whether the Pentagon should drop its ban on gays, an issue which touches one of the nation's most sensitive nerves. His lover, from San Diego, California, has written to Mr Clinton urging him to proceed as fast as possible with lifting the ban.
Gay rights groups have taken a similar view, and accuse the military leadership of covering up the killing and of fostering anti-gay sentiments in the ranks by public opposition to Mr Clinton's proposals. Opponents of the admission of gays include most of the top brass - General Colin Powell, Chairman of the Joint Chiefs of Staff, Admiral Frank Kelso, Chief of Naval Operations, and General Carl Mundy, Marine Corps Commandant.
The signs are that Mr Clinton will deliver on his election promise to end the gay ban, even though it will put him on a collision course with the biggest institution under his command. Les Aspin, the defense secretary-designate, said during confirmation hearings that the administration planned to lift the ban, addressing the issue 'very, very carefully' and 'very, very deliberately'.
But the incident also raises questions about how the military, which contains some rabidly anti- gay elements, would respond to an end to the ban, which has led to 15,000 people being thrown out of the military in recent years. Schindler's mother has been quoted saying that she fears for the lives of homosexuals in uniform if the Clinton administration allows gays to join up.
Her view appears to be confirmed by a disturbing report this month in the Navy Times, in which an unidentified US marine is asked how he would react if he discovered a homosexual was living in his barracks. 'I'd have to kill him, I guess,' was the reply.