On Saturday, the UN-backed government forces announced shooting down a fighter jet of the east-based army in the western city of Zawiya, some 45 km west of the capital Tripoli, and capturing its pilot.
"Based on social media reports about capturing a pilot of Haftar (commander of east-based army), you are ordered to immediately and urgently start an investigation into human rights violations and misuse of the Interior Ministry (powers)," the minister addressed the Zawiya Security Directorate.
The minister also ordered to replace the head of the security force that captured the pilot.
Libyan social media posted photos of the captured pilot who was being beaten and stripped off of his military uniform.
The east-based army condemned the mistreatment of the pilot, stressing that the mistreatment "violates the Geneva Convention for the treatment of prisoners of war."
The east-based army has been leading a military campaign since early April in and around Tripoli, in an attempt to take over the capital city and overthrow the UN-backed government.
The armed conflict has killed and injured thousands of people, while displacing nearly 120,000 civilians.
On Dec. 5, UN-backed Libyan Prime Minister Fayez Serraj said there will be no cease-fire without the withdrawal of the rival east-based army from western Libya.