Sufyan Qudah, a spokesman of the Jordanian Foreign Ministry, said the incursions are "a flagrant and unacceptable” breach of a long-standing status-quo agreement that limits the presence of non-Muslims at the site and permits only Islamic religious practice there.
The Waqf Council, a division of the Jordanian government, called the incursions “clear-cut proof that Al Aqsa is under great danger”.
The mosque, the third holiest site in Islam, is the most sensitive flashpoint in the Israel-Palestine conflict. The compound is also sacred for Jews because it is widely believed to be the historic site of Jewish temples.
The mosque fell under Jordanian authority after Israel was created in 1948. Israeli captured the site in East Jerusalem in the 1967 war but allowed it to remain under Jordanian administration.
The kingdom claims custodianship of the mosque and has previously criticised Israeli breaches at the site.
The ministry also criticised Israeli restrictions on Palestinians trying to access Al Aqsa.
“Israel has no sovereignty over occupied East Jerusalem and has no right to impose restrictions on the entry to the holy compound,” Mr Qudah said.
On Tuesday morning, Palestinian presidency spokesman Nabil Abu Rudeineh echoed Jordan’s criticism, saying Jews who enter the site risk deteriorating the region’s security.
Palestinian Christians, clergy and pilgrims have also reported a surge in Israeli violence, mostly at the hands of ultra-orthodox Jews in the city for Sukkot.
Videos of Jews attacking Christians, mostly by spitting at them, were widely circulated on social media on Monday.
The tension in Jerusalem comes after a night of Israeli raids in the occupied West Bank that left dozens wounded and several arrested.
Palestinian news agency Wafa reported that two Palestinian youths were wounded and dozens experienced difficulty breathing in the village of Jalud, south of the West Bank city of Nablus.
The agency reported that clashes erupted between Palestinians and Israeli settlers after the latter attacked residents’ homes and cut down electricity poles.
Dozens of Palestinians were also wounded in clashes with Israeli forces in the nearby town of Beita.
Also on Tuesday, Israeli forces shot and detained a 15-year-old Palestinian boy south of the West Bank city of Hebron.