Deputy foreign minister Tzipi Hotovely said in excerpts from a TV interview to be broadcast today that the site holy to both Muslims and Jews was "the centre of Israeli sovereignty, the capital of Israel."
"It is my dream to see the Israeli flag flying" over Al-Aqsa, she was quoted by Israeli media as saying ahead of the broadcast on parliament's cable TV channel.
"We should raise the flag, this is Israel's capital and it is the holiest place to the Jewish people," she said.
Netanyahu's office reacted swiftly with a statement late yesterday recalling his promise to maintain the status quo which allows Muslims to pray at the site, and Jews to visit but not pray there.
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"The policy of the Government of Israel regarding the Temple Mount was expressed by Prime Minister Benjamin Netanyahu in his statement Saturday night, and nothing has changed."
"Prime Minister Netanyahu made it clear that he expects all members of the Government to act accordingly," his office said in a statement
Palestinians accuse Israel of seeking to change the long-standing practice by which only Muslims are permitted to pray at the hilltop site - sacred to both Islam and Judaism - in Jerusalem's walled Old City.
US Secretary of State John Kerry met Saturday in Amman with Jordan's King Abdullah II and Palestinian leader Mahmud Abbas and announced steps to calm tensions, including installing 24-hour security cameras at the site.
Netanyahu then issued a written statement denying any changes in practice were planned.
"Israel will continue to enforce its longstanding policy: Muslims pray on the Temple Mount; non-Muslims visit the Temple Mount," he wrote.
She later issued a statement taking sole responsibility for her remarks.
"My personal opinions are not government policy. I am committed to the policy stated by the prime minister, who declared that we would not change the status quo," she said.