"These gatherings go well beyond the norms of usual prayer," said an official Hamas spokesman.
Friday is a holy day in the Islamic faith, and prayer on this day is considered compulsory for Muslim men. Recent weeks have seen violent clashes between Fatah supporters and Hamas security forces after Friday prayers.
However, Fatah is likely to ignore the ban, which was reportedly supported by the pro-Hamas Palestinian Clerics' Association.
Hamas seized control of the Gaza Strip from Fatah in June, following violence that left over 100 dead.
Fatah is headed by Western-backed Palestinian President Mahmoud Abbas, who refuses to recognize Islamist Hamas' authority in the Gaza. Western powers have likewise consistently declined to enter into dialogue with Hamas, which calls for the destruction of the state of Israel.