The origin of the overnight strikes on the Al-Kharruba airbase, about 150 kilometres (90 miles) southwest of Benghazi, was "unknown", the official said, speaking on condition of anonymity.
The base that was hit is "where members of the Wagner group are located", the official said, adding there were "no victims".
Reports carried by Libyan and Arab news websites claimed that the strikes had been launched from aircraft that belong to the UN-recognised government in divided Libya.
But the Government of National Unity based in the capital Tripoli denied any involvement.
"We are surprised by the reports," the defence ministry said, according to Libya's Al-Massar television.
"We respect the ceasefire signed in October 2020," it added.
The ministry was referring to a truce with eastern-based military strongman Khalifa Haftar that put an end to his abortive 2019-2020 assault on the capital.
Fighters from the Wagner group, alongside others from Chad, Sudan, Niger and Syria, helped Haftar in the battle for Tripoli.
Wagner mercenaries remain active in oil-rich eastern Libya as well as the country's south, though some had left to fight in Mali or in Ukraine, supporting the Russian army's invasion.
Army chief of staff General Mohamad al-Haddad also denied the Tripoli authorities had anything to do with the strikes.
"None of our aircraft targeted any site in the east," he said, according to the Libyan news website Addresslibya. "These reports are aimed at stoking a new war between Libyan brothers and involving Libya in a regional conflict."
Libya has been torn by more than a decade of stop-start conflict since a 2011 revolt toppled strongman Moamer Kadhafi, which has also drawn in multiple foreign powers.
The North African country remains split between the interim government based in Tripoli in the west, and another in the east backed by Haftar.
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