Rebel leader Abdel Fattah Younes has complained the alliance takes hours to respond to events on the battlefield because of an overly bureaucratic process.
He claimed the alliance's inaction was allowing Colonel Muammar Gaddafi's forces to advance and was letting them kill people in the rebel-held city of Misrata "everyday".
He said: "Nato is moving very slowly, allowing Gaddafi forces to advance. Nato has become our problem."
Mr Younes also said if Nato wanted to lift Col Gaddafi's weeks-long siege in Misrata, it could have done it weeks ago.
Nato took over from a coalition led by the United States, Britain and France on March 31.
It puts the alliance in charge of air strikes targeting Col Gaddafi's military infrastructure as well as policing a no-fly zone and an arms embargo.
Mr Younes said: "One official calls another and then from the official to the head of NATO and from the head of NATO to the field commander. This takes eight hours.
Meanwhile, Sky News has returned to Zawiyah - a town which saw a bloody uprising put down by Col Gaddafi's troops a few weeks ago.
Correspondent Stuart Ramsay discovered that the mosque which had been at the heart of the rebellion was razed to the ground.
In Tripoli, government spokesman Moussa Ibrahim appeared to admit for the first time that civilians had been killed during battles in Zawiyah.
But he blamed "armed militias" rather than Col Gaddafi's troops.
Elsewhere in Libya, Nato forces have reportedly launched air strikes on government forces near the key oil town of Brega.
It came as David Cameron said there was no future for Libya while the dictator was still in charge.
The Prime Minister said: "How could there be when he's literally been trying to butcher his own people?"
Rebels said the troops' convoy of eight vehicles was hit early on Tuesday and two trucks mounted with machine guns were destroyed.
Both sides are battling for control of the key eastern port, which has changed hands several times.
Rebel attempts to fire rockets and mortars against government forces have been met with counter-attacks, sending rebel forces scrambling many miles east towards Ajdabiya.
Opposition fighters have been asking the coalition to assist them with bombardments against the dictator's troops for days.
Sky's Sam Kiley, in Ajdabiya, said: "The fact that there have been some air strikes, we believe, should be very encouraging to them (the rebels).
"(The rebels) are very anxious to take the oil terminal at Brega so they can begin to export oil through an arrangement with Qatar."
Meanwhile, Col Gaddafi's regime planned to put down protests by killing civilians before the uprising began, the International Criminal Court believes.
Anti-Libyan government demonstrations which started in February soon descended into civil war after the dictator's forces opened fire on protesters.
Court prosecutor Luis Moreno-Ocampo is to report back to the UN on May 4, and is then expected to request arrest warrants.
He said: "We have evidence that after the Tunisia and Egypt conflicts in January, people in the regime were planning how to control demonstrations inside Libya.
"They were hiding that from people outside and they were planning how to manage the crowds.
"The evidence we have is that the shooting of civilians was a pre-determined plan."
He added: "The planning at the beginning was to use tear gas and (if that failed to work) shooting."
The Libyan regime has said it is ready to discuss reforms to its political system, but insists that Col Gaddafi must be allowed to stay in the country.
Nato says its aerial onslaught has destroyed 30% of Libya's military weapons. The alliance's warplanes have flown 851 sorties since taking command of UN-backed military action last week.
