Sebha Medical Centre has confirmed that it has received nine dead bodies.
ISIL claimed responsibility of the attack in a statement and said it had targeted "Haftar's heretical militia" and liberated prisoners held on the base.
Libya has been largely divided into two factions ever since the death of its dictator Muammar Gaddafi. It has been facing infighting between rivals in which so far 390 people have been killed.
The LNA-backed parliament controls the east of Libya, while the UN-backed interim Government of National Accord (GNA) governs Libya's western region from Tripoli.
GNA has accused Haftar of the "reemergence of the Islamic State organisation"
"Ever since the offensive against Tripoli, we have warned that the only beneficiaries ... are the terrorist groups and that what is happening will offer them a fertile ground to restart their activities," said GNA in a statement.
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