The city's al-Jala hospital received the bodies of 35 people killed in the shooting, according to Human Rights Watch (HRW) and media reports.
In a statement on its website, external, HRW says there were demonstrations in at least four other eastern cities on Friday - al-Bayda, Ajdabiya, Zawiya, and Darnah - after security forces shot dead a number of protesters in the previous days.
A senior hospital official told the group: "We put out a call to all the doctors in Benghazi to come to the hospital and for everyone to contribute blood because I've never seen anything like this before."
A Benghazi resident told Reuters news agency early on Saturday that many protesters were still camped outside the courthouse. Later another eyewitness told the Associated Press that special forces had fired tear gas and cleared the area.
Benghazi residents also told the BBC on Saturday that security forces had taken critics of the government from their homes.
In al-Bayda, video footage showed bloodstained bodies in a mortuary and protesters torching a municipal building and demolishing a statue of Col Gaddafi's Green book.
In Darnah, east of al-Bayda, police stations are said to have been evacuated. Oea newspaper, owned by one of Col Gaddafi's sons, reported that demonstrators had lynched two policemen in the city.
One protester told the BBC that soldiers had switched sides in some areas and joined the demonstrations. "The soldiers say we are citizens of this country and we cannot fight our citizens," he said.
No major disturbances have been reported in the capital Tripoli, where pro-Gaddafi supporters have been demonstrating.
Amid the crackdown, the semi-independent Quryna newspaper reported that the government would replace many state executives and decentralise and restructure the government.
It was unclear whether the political move was in response to growing unrest.
Earlier, the pro-government Al-Zahf Al-Akhdar newspaper threatened that the authorities would "violently and thunderously respond" to the protests.
"The people's power, the Jamahiriya [system of rule], the revolution, and Colonel Gaddafi are all red lines and those who try to cross or come near these lines are suicidal and playing with fire," it said.
Col Gaddafi is the Arab world's longest-serving leader, having ruled oil-rich Libya since a coup in 1969.
Libya is one of several Arab countries to have experienced pro-democracy demonstrations since the fall of long-time Tunisian President Zine El Abidine Ben Ali in January. Egypt's Hosni Mubarak was forced from power on 11 February.
The British Foreign Office is now advising UK citizens against all but essential travel to Benghazi, Ajdabiya, al-Bayda, al-Marj, Darnah, Ajdabiya, Tobruk and areas bordering Sudan, Chad, Niger and Algeria.