The circumstances of his death have not yet been disclosed.
According to a CNN report, an unidentified Libyan source said al-Shibli was last seen alive on Saturday or Sunday in the custody of a local militia in Marj.
Al-Shibli had been questioned in 2013 by the FBI in the presence of Libyan authorities about the September 2012 attack on the U.S. compound in Benghazi that killed U.S. Ambassador Chris Stevens and three other Americans. Al-Shibli's suspected role in the attack is unclear.
U.S. officials told the Washington Post earlier this year they were "eager" to question al-Shibli again.
Investigators say al-Shibli had contact with members of al-Qaida in the Arabian Peninsula and was a member of the Libyan Islamist Fighting Group.
The alleged mastermind of the 2012 attack in Benghazi, Ahmed Abu Khatallah, is in U.S. custody and facing federal charges in Washington, D.C.