Several injured were also reported in the metropolitan area of Tel Aviv, and in Giv'atayim, east of the city.
Incoming aircraft have been re-routed to Ramon airport in southern Israel as Hamas launched a series of deadly rockets through the skies.
Over the years, Hamas has carried out shooting, bombing and rocket attacks in Israel.
Yair Lapid made the comments following days of clashes between Israeli police and Palestinians at the contested holy site, which is revered by Jews and Muslims.
The violence came as some Israelis were celebrating the anniversary of their country's capture of the Old City and its eastern neighborhoods in the 1967 Six-Day War.
In response, Israel deployed border guards in two mixed Arab-Jewish cities that saw unrest in previous days, including the burning of a Jewish-owned restaurant and a synagogue, the fatal shooting of an Arab man and attacks on Arab-owned cars.