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.
Israeli police accused Palestinians of "defiling and desecrating" a holy site, while Palestinian officials accused Israel of trying to divide the sensitive holy site.
Shortly afterwards, Palestinians reported brief clashes with Israeli police, just outside the mosque compound. Palestinian medics said 10 people were wounded.
Videos circulating online showed Palestinians hurling rocks and police firing tear gas and stun grenades. Others showed worshippers barricading themselves inside the mosque.
Three assailants opened fire on Israeli police in Jerusalem's Old City today before fleeing to a nearby highly sensitive holy site and being killed by security forces.