Amnesty said in a statement sources at al-Jala hospital in Benghazi had reported 28 deaths and more than 110 people injured in Thursday's protests in the city, and at least three further deaths on Friday.
Local human rights activists reported at least 15 deaths on Thursday during protests in the nearby town of Al Bayda, an Amnesty International spokeswoman said.
"This alarming rise in the death toll, and the reported nature of the victims' injuries, strongly suggests that security forces are permitted use lethal force against unarmed protesters calling for political change," said Malcolm Smart, Amnesty International's director for the Middle East and North Africa.
"The Libyan authorities must immediately rein in their security forces. Those responsible for unlawful killings and excessive force -- both the direct perpetrators and those who gave the orders -- must be identified and brought to justice," he said in the statement.
Amnesty said the sources at al-Jala hospital in Benghazi had told it the most common injuries were bullet wounds to the head, chest and neck.
Thousands of people protested in Benghazi, Libya's second city, on Friday over a security crackdown in which dozens of people were killed but which failed to halt the worst unrest of Muammar Gaddafi's four decades in power.