To the east of Tripoli, NATO bombers hit the city of Sirte to clear the way for fighters with the National Transitional Council (NTC) who are trying to capture Gaddafi's hometown.
But Gaddafi loyalists showed they were still a threat by attacking the desert oasis town of Ghadames, on the border with Algeria, NTC officials said.
A spokesman for the Tripoli Military Council said investigators had found the first physical evidence of the Abu Salim prison massacre, an event covered up for years but which ultimately helped bring about Gaddafi's downfall.
"We are dealing with more than 1,270 martyrs and must distinguish each one from the other for identification by comparing their DNA with family members," said Osman Abdul Jalil, a medical official. "It may take years to reach the truth."
According to accounts from survivors who have spoken to human rights groups, starting at dawn on June 29, 1996, guards lined up inmates in the courtyards of the Abu Salim prison .
Security men, standing on the prison rooftops, fired at the inmates with Kalashnikov rifles before using pistols at close range to finish them off.
The uprising that toppled Gaddafi was ignited by protests linked to the Abu Salim massacre. In February, families of inmates killed there demonstrated in the eastern city of Benghazi to demand the release of their lawyer.
Earlier this weekend, NTC forces had pushed to within a few hundred metres of the centre of Sirte, one of the last bastions of pro-Gaddafi resistance in Libya, but later drew back to let the NATO jets do their work.
"Yesterday our freedom fighters attacked Sirte city from two sides. That doesn't mean that Sirte is free now, but it is an indication that Sirte will be free soon," said Ahmed Bani, NTC military spokesman in Tripoli.
"I'm asking now any militiamen fighting on the side of the tyrant (to realise) that the game is over."
On Sunday, the roar of jet engines could be heard overhead, as well as sporadic booms when NATO ordnance hit targets on the ground. One strike, giving off a deep thud, released a big cloud of smoke and dust over the south of the city.
"NATO has dropped a lot of bombs today," said one rebel fighter, who declined to give his name. "You can see the planes up above. They struck along here," he said, gesturing with his hand across the area south of the city centre.
NATO's support for the anti-Gaddafi rebellion played a major part in toppling Gaddafi and the alliance says it will keep up its operations for as long as needed.
In a statement, the alliance said its sorties on Saturday in the vicinity of Sirte had struck targets including 2 command and control facilities, a military staging area, a storage bunker and radar facility, and 29 armed vehicles.
There was little fighting on the ground west of Sirte, where NTC fighters have advanced closest to the city centre .
On the eastern side , the forces pushed to within 15 km, an advance of more than 25 km. A Reuters reporter there said the NTC forces had been helped by heavy NATO bombing.
She said she could hear the sound of artillery fire and see black smoke on the horizon.
Taking Sirte would be a huge boost for the NTC as it tries to establish credibility as a government, and a blow for Gaddafi, widely believed to be on the run inside Libya.
But it is an awkward proposition because pro-Gaddafi fighters there are well armed and many of the residents have family and tribal ties to Gaddafi.
Accounts from NTC fighters and people who had left Sirte indicated that pro-Gaddafi forces were trying to prevent civilians from fleeing, effectively using them as human shields.
"Gaddafi's forces have surrounded the area, closed it off, by shooting at people," said a man called Youssef, who was driving away from Sirte with his wife. "There are a lot of people who want to get out but can't."
He said he and the other civilians from Sirte leaving the city on Sunday had escaped by cutting through the desert.
That was echoed by a man called Abubakr, who was heading out of Sirte with his wife and four children in a car loaded with baby diapers and food.
"The situation is not good, really it is not good. It is terrible. There are (pro-Gaddafi) gangs unloading on people, shooting at them. It's really bad," he said.
The attack by pro-Gaddafi forces on Ghadames underlined the fragility of the NTC's grip even on parts of the country nominally under its control.
The town, about 600 km (400 miles) south-west of Tripoli, is near a border crossing that pro-Gaddafi Libyans have used to flee into Algeria. Its old town, an intricate maze of mud walls, is listed as a UNESCO world heritage site.
"These militias have attacked our people in Ghadames city ... All the information we have got is that these groups are related to the son of Gaddafi, Khamis," the NTC's Bani told a news conference.
"Our freedom fighters have taken control of that area," he said, though he acknowledged the clashes were not completely over. "This problem will end soon. It's a matter of days."
A month after ousting Gaddafi's forces from Tripoli and most of the country, the NTC is now facing challenges to its rule from only two main locations, Sirte and Bani Walid, a town about 170 km (105 miles) south-east of Tripoli.
Until both are captured, Libya's new rulers say they cannot begin the process of holding the first elections.
That leaves the country in limbo where the only real authority comes from disparate factions of anti-Gaddafi fighters who are still armed and want a stake in the new Libya.
Attempts to capture Bani Walid have ended in chaos, and now the anti-Gaddafi forces appear to have switched their focus instead to taking Sirte.
"The symbolism of a Sirte victory would be much greater than winning Bani Walid," said Geoff Porter, an independent U.S. expert on North Africa. "The collapse of Gaddafi's hometown would reverberate amongst the dead-enders and could facilitate the fall of Bani Walid".