The Libyan rebels' military commander was killed by his comrades while in custody after he was arrested by the opposition's leadership on suspicion of treason, a witness said.

The killing of Abdel-Fattah Younis raised fear and uncertainty in Benghazi, the de facto rebel capital. Thousands marched behind his coffin, wrapped in the rebels' tricolour flag, to the graveyard for his burial, chanting that he was a martyr "beloved by God". Troops fired a military salute as the coffin arrived, and angry and grieving supporters fired wildly into the air with automatic weapons.

At the graveside, Mr Younis's son Ashraf broke down, crying and screaming as they lowered the body into the ground and - in a startling and risky display in a city that was the first to shed Muammar Gaddafi's rule nearly six months ago - pleaded hysterically for the return of the Libyan leader to bring stability. "We want Muammar to come back! We want the green flag back!" he shouted at the crowd, referring to Gaddafi's national banner.

Mr Younis's death appeared to shake both the rebels' leadership body, the National Transitional Council, and its Western allies, who have heavily backed the rebels controlling most of eastern Libya.

Two weeks ago, 32 nations including the US made a major commitment by formally recognising the opposition as the country's legitimate government - a significant boost after many allies hesitated in part because the rebels, a mix of tribes and factions, were largely an unknown quantity. Those Western worries are likely to have been deepened if Mr Younis's killing opens major splits among the fractious rebels.

Mr Younis's body was found on Thursday, dumped outside Benghazi, along with the bodies of two colonels who were his top aides. They had been shot and their bodies burned.

Mr Younis was Gaddafi's interior minister until he defected to the rebellion early in the uprising, which began in February, bringing his forces into the opposition ranks. His move raised hopes among rebels and Western allies that the uprising could succeed in forcing out the country's ruler of more than four decades. But some rebels remained deeply suspicious that he retained loyalties to Gaddafi.

The National Transitional Council says it is investigating the killing. It blamed unidentified "gunmen" and has made no confirmation that Mr Younis had been arrested. It has said only that Mr Younis was gunned down on route to Benghazi, where he had been summoned to discuss "a military matter".

But a rebel special forces officer under Mr Younis's command told the Associated Press that Mr Younis was taken before dawn on Wednesday from his operations room at Zoueitina, just east of the main front with Gaddafi's forces.

Fighters from a rebel faction known as the February 17 Martyr's Brigade came to the operations room and demanded Mr Younis come with them for interrogation, said the officer, Mohammed Agoury, who said he was present at the time. Mr Agoury said he tried to accompany his commander "but Younis trusted them and went alone". "Instead, they betrayed us and killed him," he said.