Israel set up the new security measures last week after Arab gunmen opened fire from the shrine, killing two Israeli policemen. It said they were a necessary measure to prevent more attacks and were deployed routinely at holy sites around the world.
But Muslims alleged Israel was trying to expand its control at the Muslim-administered site and have launched mass prayer protests.
Major General Yoav Mordechai, who heads the Israeli defence body for Palestinian civilian affairs, said Israel was open to alternatives to lower the tensions.
"The only thing we want is to ensure no one can enter with weapons again and carry out another attack," he said. "We're willing to examine alternatives to the metal detectors as long as the solution of alternative ensures the prevention of the next attack."
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However, the Mufti of Jerusalem, Sheikh Muhammad Hussein, told the Voice of Palestine he demands a complete return to procedures that were in place before the initial attack at the shrine, known to Muslims as the Noble Sanctuary and to Jews as the Temple Mount.
Disputes over the shrine, revered by Muslims and Jews, have set off major rounds of Israeli-Palestinian confrontations in the past.
On Friday, several thousand Palestinians clashed with Israeli security forces in the West Bank and in Jerusalem after noon prayers, the centrepiece of the Muslim religious week. Three Palestinians were killed and several dozen wounded.
Late on Friday evening, a 20-year-old Palestinian identified as Omar al-Abed jumped over the fence of the Halamish settlement and entered a home, surprising a family that was celebrating the birth of a new grandchild during their traditional Sabbath dinner.
Prime Minister Benjamin Netanyahu denounced the attack as "an act of terror, carried out by a beast who was incited with unfathomable hatred."
Al-Abed said in a pre-attack Facebook post that he expected to be killed in the attack and his father said he was motivated by the violence at the Jerusalem shrine.