Several militia groups angrily accused Zidan's government of colluding with the U.S. in the operation and allowing foreigners to seize a Libyan on its own soil.
The Libyan government said the al-Libi raid was carried out without its knowledge. But its response has been mild. It asked Washington for "clarifications" about the raid.
Some militiamen are convinced Zidan allowed the raid.
"I can't imagine why everyone is standing by Zidan, who is a traitor who handed a Libyan civilian over to the Americans," said Jamal al-Haji, who belongs to a militia-linked group in Tripoli.
On Tuesday, Zidan said the Libyan government had requested that Washington allow al-Libi's family to establish contact with him. Zidan insisted that Libyan citizens should be tried in their homeland if they are accused of crimes.
He was abducted hours after meeting Wednesday evening with al-Libi's family.
Zidan said relations with Washington, a key ally, would not be affected.
White House spokesman Jay Carney said the U.S. condemned Zidan's kidnapping. U.S. Secretary of State John Kerry said he was pleased to hear of Zidan's release and that Washington was helping the Libyan government build its security capacities.
"Libyans did not risk their lives in the 2011 revolution to tolerate a return to thuggery," he said in a statement.
The apparent backlash against the government over the al-Libi raid could make Tripoli even more wary of allowing Washington to go after other wanted militants on Libyan soil. In particular, the U.S. has sought the arrest of militants behind the Sept. 11, 2012, attack on its consulate in Benghazi that killed the ambassador and three other Americans. Some of the suspects live openly in the eastern city, but the state is powerless to pursue them.
The two militia groups who said they were involved in Zidan's abduction were originally formed by Nouri Boushameen, the head of the National Congress, or parliament, with the intent of providing security in the capital.
Boushameen sought to distance himself from the abduction, telling a news conference before Zidan's release that any members of the groups involved would be punished. He said he visited Zidan in captivity and told him he was working for his release.
Zidan and members of his government have increasingly spoken of trying to rein in militias, to little effect. The groups have lashed out at the government before and regularly defy its authority.
Just last month, militiamen abducted the son of the defense minister in a move seen as aimed at preventing any action against the groups. Several weeks ago, the militia of al-Tajouri, which rescued Zidan, seized the daughter of the Gadhafi-era intelligence chief and held her briefly. Earlier this year, militiamen besieged government buildings for days to pressure lawmakers to adopt a law banning Gadhafi-era politicians from holding any posts.
Since Gadhafi's ouster and death, the groups have grown and multiplied. Many tout themselves as defending the "revolution's goals," but often act to protect fiefdoms they have carved out and are accused of blackmailing or intimidating citizens.
Others have Islamic extremist ideologies and are suspected of links to al-Qaida and other militant groups across North Africa and into Egypt.