In an interview with NBC News, Megaryef said the attackers fired rocket-propelled grenades and mortar rounds with such accuracy that the attack had to have been planned and carried out by experienced militants.
When asked if the offensive anti-Islam movie – which sparked violent protests across the Muslim world – had anything to do with the assault, Megaryef replied: "Not on this attack."
"Reaction should have been, if it was genuine, should have been six months earlier. So it was postponed until September 11," he said in an interview conducted in English.
"They chose this date, 11th of September, to carry a certain message."
The attack on the consulate, which killed US ambassador Chris Stevens and four other Americans, was initially said to have been part of a protest over the film, but the White House later called it a "terrorist attack".
Megaryef told NBC there were no protesters at the consulate before the attack, which he said came in two waves – with militants firing grenades at the consulate and then attacking an annex with mortar rounds.
"It's a pre-planned act of terrorism," he said, adding that the film had "nothing to do with this attack".
Libyan officials were quick to condemn the attack and have vowed to help the United States bring the perpetrators to justice.
Libya's newly elected government is struggling to rein in the patchwork of local militias – some led by hardline Islamists – that emerged during last year's uprising, which toppled longtime dictator Muammar Gaddafi.
US officials have said al-Qaeda may have been behind the consulate assault, which took place on the 11th anniversary of the September 11 attacks. – Sapa-AFP