The government in Libya says the killing of a rebel commander is proof that the rebels are not capable of running the country.
However, the National Transitional Council says the shooting of General Abdel Fattah Younes was carried out by members of the Obaida Ibn Jarrah Brigade.
The BBC reports the NTC has set up a committee to investigate the motives for the assassination.
Rebel oil minister Ali Tarhouni said General Younes and two of his aides were killed after being recalled to Benghazi for questioning. Their bodies were found on Friday.
Mr Tarhouni said the killers were still at large.
However, a government spokesman said General Younes was killed by al-Qaeda.
''By this act, al-Qaeda wanted to mark out its presence and its influence in this region,'' he said.
General Younes defected to the rebels in February after serving Colonel Muammar Gaddafi since the coup which brought him to power in 1969.
A BBC reporter in Misrata says the killing will feed international suspicions that the rebels cannot be trusted.