Unknown assailants fired four rockets at the international airport just outside Labraq, from which General Khalifa Haftar's forces launch raids against Islamist positions in the east.
The airport, which has civilian and military terminals, has been targeted repeatedly in recent months.
Labraq is some 65 kilometres west of the Islamist stronghold of Derna, which was hit on Monday by Egyptian and Libyan warplanes.
The raids were in retaliation for the beheading of 21 Coptic Christians by local jihadists affiliated with the Islamic State group.
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A previous toll had put the number of dead at 40, but four more succumbed to their injuries in the hours following the attack, the ministry said.
Labraq is one of the few airports still operating in the North African country, after both the Tripoli and Benghazi facilities were put out of action in clashes.
Libya, which has been roiled by turmoil since the NATO-backed ouster of dictator Moamer Kadhafi in 2011, is awash with weapons and rival militias battling to control its cities and oil wealth.
With the capital in the hands of Islamist militias, the recognised government has taken refuge in Al-Baida, just a few kilometres west of Labraq.