Saint Porphyrios church is in the Al-Zaytoun Neighborhood of Gaza City.
Premier understands the bishop and priest were inside at the time but neither were hurt and the main damage is in the cemetery.
These pictures have been posted online but Premier has been unable to independently verify them:
Hamas militants have been firing hundreds of rockets into Israel and the country says it is bombing locations where the weapons are being held.
Officials claim the militants are hiding them in civilian areas.
More than 630 Palestinians, most of them civilians, and 30 Israelis have been killed in the past 15 days of fighting.
Meanwhile the Palestinian Prime Minister says any ceasefire deal must involve the end of an economic blockade.
Rami Hamdallah said it was time for the "siege to stop" during a visit from the UN Secretary General.
Israel and Egypt imposed a blockade on Gaza when Hamas came to power in 2007.
Ban Ki-Moon and US Secretary of State John Kerry are both in the region to try and find a peace plan.