At least seven powerful explosions were heard around 2:20 am (0020 GMT), as state television quoted a military official as saying NATO warplanes "are currently bombing civilian sites in the capital Tripoli."
In Brussels, an Atlantic alliance official said "NATO can confirm that we targeted military objectives in Tripoli this morning," and that the seven strikes were on a command and control node.
Two more explosions were heard in the same area at about midday.
The attack came after rebel forces said they lost 16 fighters east of Tripoli and that they infiltrated the capital and attacked a regime command post where a son of the strongman was among officials targeted.
The rebel forces, who have been fighting to oust Gaddafi for more than five months, said the assault "seriously injured" a high-ranking member of Gaddafi's security forces.
"Yesterday (Thursday) in Tripoli, there was an attack on an operations centre of top regime officials, including Seif al-Islam Gaddafi," National Transitional Council vice president Ali Essawy said after a meeting in Rome with Italian Foreign Minister Franco Frattini.
"One person was left seriously injured," he said, identifying the person as a high-ranking security official.
Frattini said the "rocket attack against an operations centre" probably in a Tripoli hotel was aimed at "top officials... including Gaddafi's son Seif, and the head of the secret service, Abdullah al-Senussi."
On Thursday, unconfirmed rumours swirled that rebels in Tripoli had tried to assassinate senior regime members that day.
Since the revolution began in mid-February, a number of Tripoli-based groups have broadcast videos purporting to show acts of civil disobedience in the heavily controlled capital.
Libyan officials denied the attack occurred and denounced as "criminal and unjustified" what they said were NATO raids that killed six guards at a pipeline factory south of an oil plant in the eastern town of Brega.
"There was no attack," government spokesman Mussa Ibrahim told reporters in reference to the rebels' claims they had launched a raid on a Tripoli command post.
Rebel forces, he said, were losing their battles in the east of the country and to the southwest and trying "to boost their morale with lies and small victories".
Elsewhere, the rebels said 16 of their men were killed in two days of fighting for Zliten, the last coastal city between insurgent-held Misrata and the capital.
"Sixteen of our fighters have fallen as martyrs and 126 more have been wounded in fighting with loyalist troops in Zliten," said a rebel statement, with clashes said to be particularly heavy in the suburb of Souk al-Thulatha.
The insurgents have been trying for weeks to take Zliten, 200 kilometres (120 miles) from Tripoli and 40 kilometres west of Misrata.