Israeli Prime Minister Benjamin Netanyahu has moved to bring cabinet members into line after a deputy minister said she "dreamed" of seeing the Israeli flag flying over the flashpoint Al-Aqsa mosque compound.

Deputy foreign minister Tzipi Hotovely said in excerpts from a TV interview to be broadcast on Tuesday that the site sacred to both Islam and Judaism 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.

The compound is known to Jews as the Temple Mount.

In response, opposition Zionist Union MK Yoel Hasson called for the "messianic" Hotovely to be fired.

"Dismiss Hotovely this evening," Hasson said. "With the stubbornness of a donkey, the messianic deputy minister continues to incite the entire Middle East."

"Every few months she repeats her call to have the Israeli flag flying over the Temple Mount, as if the situation here was not sensitive enough."

Netanyahu's office reacted swiftly with a statement late on Monday recalling his promise to maintain the status quo which allows Muslims to pray at the site, and Jews to visit but not pray there.

"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 in Jerusalem's walled Old City.

The comments come as tensions over the site sparked a wave of violence that has seen knife and gun attacks against Israelis, as well as clashes between Palestinians and Israeli security forces.

US Secretary of State John Kerry met on Saturday in Amman with Jordan's King Abdullah II and Palestinian leader Mahmoud 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.

In stark contrast, Hotovely, from Netanyahu's right-wing Likud party, told Knesset TV that Jews should be allowed to pray there.

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.

Early on Tuesday, Israeli forces detained at least 44 Palestinians in multiple raids across the West Bank, Maan news agency reported.

According to an Israeli army spokesperson, those arrested included two in Jenin, three in Nablus, one in Qalqiliya, 10 in Ramallah, 12 in Bethlehem, and 15 in Hebron.

So far well over 1,000 Palestinians have been arrested by Israeli forces since the beginning of the month, with more than half of those in the West Bank, according to Palestinian rights groups.

Prisoner rights group Addameer has estimated that there are currently around 6,300 Palestinians in Israeli prisons.