"The perimeter of the Ministry headquarters in Tripoli was brutally attacked by air force of Haftar's forces (east-based army) Thursday afternoon," the ministry said in a statement.
"The Ministry condemns this cowardly attack that clearly reveals the true intention behind the military campaign against the capital," the statement said.
"The Ministry considers today's attack more clear evidence to the criminality of the military leadership, the targeting of the state's institution and indifference to the lives of civilians," it said.
The east-based army's information office said that its fighter jets have targeted positions of the UN-backed government forces in southern Tripoli, where the ministry is located, destroying operation chambers and weapon stores.
The east-based army, led by General Khalifa Haftar, has been leading a military campaign in and around Tripoli since early April, attempting to take over the city and topple the UN-backed government.
The armed conflicts have injured and killed thousands of people, and displaced nearly 120,000 civilians.