The ruins, which are said to date back from the Byzantine era, were found by accident by workers constructing a new shopping centre.
Heyam al-Bitar, research director for the Hamas-run Tourism and Antiquities Ministry, said on Tuesday that the discovery included remnants of marble Corinthian pillars, foundations and crowns, some of them with a Greek cross.
She says they date back to the sixth century, and are characteristic of the era of Emperor Justinian.
The antiquities are to be taken to the ministry's museum for further study.
The Gaza Strip is predominantly Muslim however it is home to a small Christian community.