Nonetheless, the decision marks something of a sea change at the Mount, where all Jewish prayer has long been subject to an unofficial prohibition.
The site is also home to the al-Aqsa Mosque and is under the auspices of the Jerusalem Waqf, which is overseen by Jordan.
By agreement with the Israeli government, which administers access to the site, religious Jews are allowed to enter in groups of 50 at a time and Jewish tourists can visit for up to four hours, five days a week.
In return, though, previous governments have maintained a ban on Jewish prayer.
Prime Minister Netanyahu, though, has now backed efforts to reverse this, instigated by National Security Minister Itamar Ben-Gvir.
Ben-Gvir, the leader of the far-right Otzma Yehudit party and the minister responsible for policing, has himself been pictured praying at the Mount and even suggested building a synagogue there.
Asked about prayer policy earlier this month, Netanyahu said: "The changes Ben-Gvir is making are not changing the status quo and it is in coordination with me. I decide on the policy."