General Muhammad Ali Ahmad al-Haddad was in Ankara for high-level defence talks aimed at boosting military co-operation between the two countries.
The plane landed "safely without incident" and no one was transported to a hospital, according to airport officials.
An airplane has, for the first time, automatically landed itself after an in-flight emergency, according to the system’s manufacturer.
Libyan Prime Minister Abdul-Hamid Dbeibah has confirmed the death of Libyan military chief Muhammad Ali Ahmad al-Haddad and four others in a plane crash in Turkey on Tuesday evening.