The foreign ministry said it "strongly condemned Thursday's attack on the Egyptian church ... and the aggression towards Father Paul Isaac and his assistant by the irresponsible armed men," LANA quoted a foreign ministry statement as saying.
It did not elaborate on the attacks but said an inquiry committee involving the interior, defense and justice ministries had been formed and had "taken the necessary measures to secure the church and its occupants."
Libya's small Christian community has expressed fears over Islamist extremism as the government struggles to impose its authority over armed groups which have refused to lay down their weapons since the 2011 war that ousted Moammar Gadhafi.
In December, an explosion at a building belonging to a Coptic church in Dafniya, close to the western city of Misrata, killed two Egyptian men and wounded two others.
Last month, four foreigners were arrested in Benghazi on suspicion of being Christian missionaries and printing books about Christianity.
Hussein Bin Hmeid, a spokesman for the government-affiliated security apparatus called the Preventative Security which made the arrests, said the missionaries had since been transferred to Tripoli.
He said the four—an Egyptian, a South African, a Korean and a Swede who was traveling on a U.S. passport—were now in the hands of the Interior Ministry and had been visited by representatives from their countries.