"We urge the Palestinian and Israeli sides to exercise restraint and take immediate steps to prevent further escalation of the situation in East Jerusalem," the ministry said in a statement.
The ministry said that any ill-conceived action could trigger extremely negative consequences.
"Worsening tensions around Jerusalem’s holy shrines threaten to further postpone a fair, legal solution to the Palestinian problem, and escalate the situation in the Middle East and North Africa," the ministry said.
On Tuesday, Palestinian youths again barricaded themselves inside the al-Aqsa mosque and threw stones at Israeli security forces. Clashes flared early Sunday after Israeli police launched a late-night search operation for hidden explosives in contested East Jerusalem. Officers ended up pursuing masked Arab teens who holed up at the shrine.