The decision was taken Thursday at the behest of Prime Minister Benjamin Netanyahu, The Jerusalem Post said.
"We intend to change the norm that has taken root here where it is possible to throw lethal and murderous objects in Israel without an answer or impediment. This will change," Netanyahu was quoted as saying.
Under the new rules, protesters will be sentenced to a minimum of four and up to 20 years in prison for throwing stones, Molotov cocktails, firecrackers and other objects deemed to be harmful.
On Thursday, a police operation in East Jerusalem led to the arrest of over a hundred protesters. Unrest flared on September 13, after a group of Arab youths barricaded themselves inside a mosque in Jerusalem’s Temple Mount complex and threw stones at Israeli security forces.