By the time he arrived in Vietnam in late December 1967, Thompson was a 25-year-old chief warrant officer reconnaissance pilot with the 123rd Aviation Battalion. On March 16 1968, he was flying his H-23 scout helicopter, with its three-man crew, over a part of Quang Ngai province known as Pinkville, supporting a three company search-and-destroy assault on several villages, which faulty intelligence had indicated were heavily defended by Vietcong troops. The US 1/20th Infantry Battalion attack was led by Charlie Company, commanded by Captain Ernest Medina, who sent in the 1st platoon, led by Calley, to clear out My Lai and several neighbouring hamlets.
Charlie Company was bent on revenge; days earlier several of its members had been killed by Vietcong mines and booby traps. Without a shot being fired against them, Calley's men began slaughtering anyone they could find - old men, women and children. Groups of villagers, 20 and 30 at a time, were lined up and mown down. In the four-hour assault, the men of the 2nd and 3rd platoons joined in.
Early on, Thompson spotted a young woman injured in a field. He dropped a smoke cannister to indicate she needed medical help; he claimed in a court martial later that Medina went over and shot her. During the massacre, Thompson discovered the bodies of 170 executed villagers in a drainage ditch. One of his crew rescued a child and flew it to hospital at Quang Ngai.
In another incident, he challenged Calley to help a group of civilians hiding in a bunker rather than attack them. When Calley refused, Thompson ordered his helicopter gunners to open fire on the 1st platoon if they advanced any closer. He then called down gunships to rescue the civilians.
On returning to Chu Lai military base, Thompson reported everything to his commanding officer. But a local inquiry whitewashed his complaints, claiming the civilian deaths had been caused by artillery fire. An elaborate cover-up ensued and Thompson was awarded the Distinguished Flying Cross for saving the lives of Vietnamese civilians "in the face of hostile enemy fire" - he threw the medal away, believing his commanders wanted to buy his silence.
A year later, the Pentagon learned the truth and a high-level inquiry was conducted by Lieutenant General William Peers. Thompson later appeared as a witness at the courts martial of several men involved in the massacre or the cover-up, though the only person convicted was Calley, who served a few months in jail before having his life sentence reduced and being given parole.
During his time in Vietnam, Thompson was shot down five times, finally breaking his backbone. He received a commission, but back in America some colleagues regarded him as a turncoat. When evidence of the atrocity was finally made public in late 1969, he was castigated by pro-Vietnam war politicians in Washington.
It was only 30 years later that Thompson was recognised as a genuine American hero by the Pentagon, after a nine-year letter-writing campaign. The US army had initially wanted his Soldier's Medal, the military's highest award for bravery in peacetime, to be presented quietly, preferring to keep what happened at My Lai in the background. But Thompson resisted. He wanted a ceremony at the Vietnam memorial in Washington, DC, and the bravery of his fellow crew members recognised as well. In March 1998, he finally got his wish.
Thompson was born in Atlanta, Georgia, to strict Episcopalian parents, and moved to nearby Stone Mountain when he was three years old. His father served with both the US army and navy during the second world war and spent 30 years with the naval reserve. His paternal grandfather was a full-blooded Cherokee Native American, forced off tribal land in North Carolina in the 1850s and resettled in Georgia. Thompson joined the US navy in 1961, and spent three years with a Seebees construction unit. After a brief return to civilian life in 1964, during which he became a funeral director, he re-enlisted in the army, as it was becoming engaged in Vietnam.
The My Lai experience affected him badly. He grappled with alcohol and had several failed marriages. After service in Korea, he returned to the US, dropping the name Hugh and calling himself Buck as a way of distancing himself from past events. He left the army briefly and then re-enlisted, flying with medical evacuation units and instructing trainee pilots. He retired from the army in November 1983 and worked as a helicopter pilot for oil companies in the Gulf of Mexico. Later he was involved with the Louisiana department of veteran affairs for six years, giving lectures to students and schoolchildren and speaking about ethics to military academies.
After his role in trying to stop the massacre was recognised in the US, Thompson and his surviving crew member, Larry Colburn, were taken back to My Lai, where they were introduced to three women who had survived the massacre. On a second visit three years later, he met an electrician from Ho Chi Minh City who, aged nine, had been one of the children Thompson had rescued from the bunker.
Thompson is survived by three sons and his partner Mona Gossen.