The ministry said: "It is a humanitarian and legal obligation to respect the sanctity and historical status of the religious sites in the Israeli occupied East Jerusalem, especially Al-Haram Al-Sharif".
They said they were still working to identify the attackers.
Jerusalem Police Commissioner Yoram Halevy said the three gunmen - who were Arab citizens of Israel - were calculating and methodical in their attacks.
Just a few short hours later, as the Druse families began their mourning, Jordan began negotiating with Israel in an attempt to reopen the Temple Mount to Muslim visitors.
Muslims revere it as the Noble Sanctuary, and Jews know it as the Temple Mount.
Rivlin called on the Arab leaders both inside and outside of Israel "to express a clear position against this criminal attack". The attack is still under investigation and will force us to look into existing security arrangements at Temple Mount and in its vicinity. It is considered the third-holiest site in Islam and the holiest in Judaism.
Three Palestinian men, armed with Carlo submachine guns and a handgun, fired toward police officers close to the Lion's Gate entrance to Jerusalem's Old City. Worshippers dispersed after the prayers without incident. They shot at them and escaped in the direction of the mosques on Temple Mount.
The grand mufti of the city, Mohammed Hussein, was detained for questioning Friday at a police station in the Old City, his son, Omar, told The Associated Press.
Friday's shooting from inside the walled compound in Jerusalem's Old City killed two Israeli policemen.
Israeli authorities say most of the Palestinians killed were carrying out knife, gun or car-ramming attacks.
"Forbidding the Friday prayer is an unfair procedure", Keswani said.
In a condolence statement, Israeli Prime Minister Benjamin Netanyahu said, "This is a sad day for our brothers in the Druze community who are paying the heaviest price in our shared duty to defend the security of Israel". Violent clashes on the Temple Mount have been the spark for prolonged and deadly waves of Israeli-Palestinian violence in the past. This marked the first time in 17 years that the mosque was closed for Friday prayers.