"Jordan considers such serious and outrageous actions by Israel an unprecedented escalation," said Ambassador Dina Kawar in a letter to the president of the Security Council.
Noting that Jordan had recalled its ambassador from Israel, the UN envoy added that "this is without prejudice to any further lawful steps and measures that Jordan will be taking to stop Israeli attacks against the Haram Al-Sharif (Al-Aqsa)" mosque.
Meanwhile, Palestinian representative to the United Nations Riyad Mansour said the 15-member council must "adopt a position to call on the Israeli government to stop all these activities and policies of provocation and incitement."
The request for a statement from the council came after renewed clashes earlier Wednesday between Israeli police and Palestinians at the Al-Aqsa mosque and a car attack by a Palestinian driver who rammed his car into a group of pedestrians, killing a border policeman.
Mansour blamed the latest confrontation at the Al-Aqsa mosque on "extremists" who entered the mosque, some without taking their shoes off, which he said "is extremely provocative."
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"They are trying to push the region into religious confrontation," Mansour told reporters after meeting with Australian Ambassador Gary Quinlan, whose country chairs the Security Council this month.
Kawar said in her letter that Israeli special forces had stormed the mosque compound, firing tear gas and rubber bullets in what she described as a "blatant and unlawful use of force against one of the holiest sites on Earth for Muslims."
Quinlan said there was no request for an emergency council meeting but that there were discussions on the mounting tensions in east Jerusalem.
Israel's UN Ambassador Ron Prosor sent a letter to the council accusing the Palestinians of incitement and noting that there had been no UN condemnation of Palestinian attacks on Israelis.
Al-Aqsa has been the scene of frequent confrontations in recent months, largely triggered by Palestinian fears that Israel was poised to allow Jewish prayer at the site.