Reports say Nato targeted government buildings, including the compound of Libyan leader Col Muammar Gaddafi.
Baroness Amos told the UN that the besieged city of Misrata was in a dire state, short of food and water.
About 750,000 people have fled Libya since the uprising began in February.
The bombardment of Tripoli was the heaviest for several weeks. Reports say four buildings were targeted, including Col Gaddafi's family complex, the military intelligence agency and state TV headquarters.
The government said the country's high commission for children had been hit, and four children were injured by flying glass. It is impossible to verify the reports.
Nato says it has carried out 6,000 air strikes since it began enforcing a UN-mandated no-fly zone over Libya in March.
The alliance said again it was not targeting Col Gaddafi himself, but rather hitting command and control bunkers.
Baroness Amos says the UN is looking into "conflicting" reports about the plight of refugee ships leaving LibyaIt said it had significantly downgraded Col Gaddafi's ability to launch attacks, and called for the Libyan leader to step down.
The BBC's Bethany Bell in Brussels, where Nato has its headquarters, says there are questions about whether Nato's strategy is working.
The alliance admits this conflict will not be solved by military means alone, our correspondent says, but for now, an exit looks neither quick nor easy.
Rebels in Misrata, the biggest western city outside Libyan government control, say they have pushed pro-Gaddafi troops back from its outskirts.
On Tuesday, Nato said it had destroyed more than 30 military targets in the Misrata area, including a dozen main battle tanks, three rocket launch systems and 15 ammunition storage sites.
"Although it's a real challenge for us to strike military targets in and around population centres like Misrata, while minimising the risks to innocent civilians, we have been working hard to prevent attacks by pro-Gaddafi forces," Nato spokesman Brig-Gen Claudio Gabellini said.
Misrata has been under siege for two months.
'Widespread shortages'Baroness Amos said the disruption caused by a combination of the conflict and sanctions was paralysing the country.
Continue reading the main storyAn official from Libya's rebel administration - a volunteer like so many in this DIY revolution - has been trying, with a biro, to explain the chain of command that is, or should be, emerging from the chaos ”End Quote Andrew Harding BBC News, Benghazi She called on the Security Council to ensure that all parties respected international law and she said the use of cluster bombs, sea and land mines, as well as aerial bombing showed a callous disregard for civilians.
The conflict and disrupted supply lines had delayed the arrival of commercial goods, she said.
"Widespread shortages are paralysing the country in ways which will impact gravely on the general population in the months ahead, particularly for the poorest and the most vulnerable," she added.
There was only enough food left for a few months, she said.
She renewed calls for money, saying an appeal for $144m (￡88m) had only been half met, and more than that would be needed.
A Red Cross ship successfully docked in Misrata on Monday, bringing medical equipment, baby food and spare parts for electrical and water systems.
The port has become a lifeline for the city, allowing refugees to leave and supplies to be brought in, but has come under repeated attack from pro-Gaddafi forces.
Medical sources say at least 300 people have been killed by the weeks of fighting in Misrata.
'Keep going'The rebels say Misrata remains surrounded, but that they have advanced about 30km (18 miles) to the west.
An AFP correspondent in Misrata said the rebels were now in control of a stretch of coastline heading towards the capital.A rebel spokesman, Mohammed, told the BBC: "We've pushed Gaddafi away from Misrata."
He said the morale of the rebels was high, and that "they want to keep going".
Last week, a boat carrying 600 refugees broke up shortly after leaving Tripoli port.
It is not clear how many people died, but eyewitnesses reported seeing bodies, wreckage and survivors swimming back to shore.
The UNHCR has called on all ships using the Mediterranean to be prepared to offer assistance to the often unseaworthy vessels carrying migrants from Libya to Europe.
At least three other boats have been reported missing in the Mediterranean.
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