Updated at 4 p.m. ET
BENGHAZI, Libya - The commander of the Libyan rebels' military was killed by fellow rebels while in custody after he was arrested by the opposition's leadership on suspicion of treason, witnesses said Friday, indicating a potentially major split in the ranks of the movement battling Muammar Qaddafi.
The killing of Abdel-Fattah Younis under still mysterious circumstances raised fear and uncertainty in Benghazi, the de facto rebel capital, and worries among Western allies who have backed the rebels controlling most of the eastern Libya.
The National Transitional Council, the rebels' leadership body, has said it is investigating the killing. It blamed unidentified "gunmen" and has made no confirmation that Younis had been arrested. It has said only that 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 Younis' command told The Associated Press that Younis was taken before dawn on Wednesday from his operations room at Zoueitina, just east of the main front with Gahdafi's forces.
Fighters from a rebel faction known as the February 17 Martyr's Brigade came to the operations room and demanded Younis come with them for interrogation, said the officer, Mohammed Agoury, who said he was present at the time.
Agoury said he tried to accompany his commander, "but Younis trusted them and went alone."
"Instead, they betrayed us and killed him," he said.
Younis' 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.
The February 17 Martyrs Brigade is a group made up of hundreds of civilians who took up arms to join the rebellion. Their fighters participate in the front-line battles with Qaddafi's forces, but also act as a semi-official internal security force for the opposition. Some of its leadership comes from the Libyan Islamic Fighting Group, an Islamic militant group that waged a campaign of violence against Qaddafi's regime in the 1990s.
An officer with the rebels' internal security forces the official security force of the National Council told AP that the council ordered Younis' arrest after a letter arose earlier this week connecting the commander to Qaddafi. But he suggested the killing had not been authorized by the council and was instead an act of vengeance by rebels.
He said Younis was brought back to the Benghazi area Wednesday and held at a military compound until Thursday, when he was summoned to the Defense Ministry for questioning.
As they left the compound, two men from the security team escorting the detainees opened fire from their car on Younis with automatic weapons, said the officer, who was at the compound and saw the shooting. He said the two men were members of the February 17 Martyrs Brigade.
"The men's leader was shouting 'Don't do it!' but they shot Younis and his two aides, and took their bodies in their car and drove away," the officer said. He spoke on condition of anonymity because he was not authorized to discuss the events.
Officials from the National Transitional Council could not immediately be reached for comment on the witnesses' version of the events.
Younis was Qaddafi'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 on the rebel side remained deeply suspicious of him because of his longtime ties to Qaddafi.
Agoury said the Martyrs Brigade had an agenda against Younis, because while with the regime he was involved in the bloody crackdown that crushed the LIFG.
"They don't trust anyone who was with Qaddafi's regime, they wanted revenge," said Agoury.
A member of the Martyr's Brigade said his group had evidence that Younis was a "traitor." He told the AP that "the evidence will come out in a few days." The brigade member spoke on condition of anonymity because he feared reprisals.
On Thursday, before the commander's death was announced, rebel military spokesman Mohammed al-Rijali had said Younis was taken to Benghazi for "interrogation" on suspicion his family might still have ties to Qaddafi regime.
The city of Benghazi woke up to fierce shooting Friday morning, as the news of Younis' death spread confusion and suspicion in the city.
Thousands marched in Younis' funeral procession on Friday, as men draped the rebel tricolor flag over his coffin and carried it to a cemetery, where he was buried.
Younis' son, Ashraf, broke down, crying and screaming as they lowered the body into the ground.
"We want Moammar to come back! We want the green flag back!" he shouted at the crowd, betraying his frustration with the months of chaos in the country and a desire for a return to normalcy.
At the funeral, Younis' nephew Mohammad al-Obaidi called Younis a martyr and a champion of the Libyan uprising, while the crowd broke into chants of "The martyr is God's beloved" and "Allah is Great."
At the cemetery, Younis was given a military farewell with a 300-soldier salute beore being buried. The crackling of machine guns shot in the air competed with the crowds chanting.
Younis' deputy Col. Suleiman Mahmoud has taken over the military's duties in Benghazi.