But Ben-Gvir, whose role as national security minister includes responsibility for policing, said last May that it was his policy to allow prayer, including full prostration.
Asked about the prayer policy on Monday, Netanyahu denied that it was a breach of the long-held arrangement with the Waqf.
"The changes Ben-Gvir is making are not changing the status quo and it is in coordination with me. I decide on the policy,” he told reporters.
Ben-Gvir has also previously suggested the building of a synagogue on the mount, which drew condemnation from Washington, albeit under the Biden administration.
Then-State Department spokesperson Matthew Miller said at the time: “The ongoing reckless statements and actions of this minister only sow chaos and exacerbate tensions at a moment when Israel must stand united against threats from Iran and its proxy terrorist groups, including Hamas and Hezbollah.
"They directly undermine Israel’s security.”
Netanyahu’s comments came after he reportedly clashed with Deputy Attorney General Gil Limon during a cabinet meeting on Sunday after the legal official demanded Ben-Gvir be sacked over alleged interference in police matters – a claim Ben-Gvir has strongly denied.
According to Ynet, Netanyahu called Limon’s comments “simply embarrassing” and insisted that Ben-Gvir’s firing “will not happen”.
With the next set of Israeli elections due by October, the prime minister currently depends on the support of Otzma Yehudit to maintain his coalition’s Knesset majority.
The latest polls have the party winning between seven and ten seats at those elections, which would likely prove the difference between a majority for the current government bloc and one for the opposition.