The strike on Thursday damaged the Holy Family Church, the only Catholic Church inside the Palestinian enclave.
The Vatican did not immediately respond to a request for comment.
The Israeli Defence Forces said it was looking into the matter.
Italy's ANSA news agency said six people were seriously injured, while parish priest Father Gabriele Romanelli, who used to regularly update the late Pope Francis about the Israeli-Palestinian conflict, suffered light leg injuries.
"Israeli raids on Gaza have also hit the Holy Family Church," Italian Prime Minister Giorgia Meloni said in a statement on X.
"The attacks against the civilian population that Israel has been carrying out for months are unacceptable. No military action can justify such an attitude."
In the last 18 months of his life, Francis would often call the lone Catholic church in the Gaza Strip to see how people huddled inside were coping with a devastating war.
The war began with Hamas's cross-border attack on October 7, 2023.
That day, militants killed some 1200 people, mostly civilians, and abducted 251 people, most of whom have since been released in ceasefire agreements or other deals.
Fifty hostages are still being held, less than half of them believed to be alive.
Israel's retaliatory offensive has killed more than 58,000 Palestinians, according to Gaza's health ministry, which has said women and children make up more than half of the dead.
with AP
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