More than a hundred people were wounded on Thursday, the agency said.
There were also reports of clashes in Jerusalem between Israeli security forces and Muslim worshippers following Friday prayers at the al-Aqsa Mosque.
Mr Trump’s decision on Wednesday to recognise Jerusalem as Israel’s capital will be discussed at a special UN Security Council meeting at 4 pm UK time.
It was called at the request of Britain, France, Italy, Egypt and four of the other 15 members of the council.
A senior Palestinian Authority official said that American vice-president Mike Pence, who is scheduled to visit the region this month, was “not welcome”.
But the White House said that Mr Pence still intends to meet Palestinian Authority President Mahmoud Abbas “and thinks any decision to pull out of the meeting would be counterproductive”.
There were protests against the move across the Muslim world on Thursday.
More than 5,000 people marched near the Chatila refugee camp south of Beirut, Lebanon, carrying Palestinian flags.
Thousands were also on the streets of Egypt, Jordan and Turkey.
