The kingdom has custodianship over the site, one of the holiest places in Islam. It is a major flashpoint in the conflict between Palestine and Israel, which has also marred Israel's ties with Jordan.
Hundreds of Israelis entered the site this week, at the start of the the Jewish holiday of Sukkot, the Palestinian religious endowments department said.
Sufian Qudah, a Jordanian Foreign Ministry spokesman, said the ministry sent an official memorandum to the Israeli embassy in Amman protesting against "incursions by the militants and the settlers and Israeli Knesset members into the holy Al Aqsa Mosque".
Mr Qudah said "Israeli police protection" provided them with cover.
Mr Qudah said Israel, as the occupying power in Jerusalem, is obliged to refrain from measures that affect the sanctity of the mosque.
He said the compound is "a place of worship exclusively for Muslims". The site is also sacred for Jews.
It fell under Jordanian authority after Israel was created in 1948. Israel captured the site in East Jerusalem in the 1967 war but allowed it to remain under Jordanian administration.
A large proportion of Jordan's 10 million population are descendants of Palestinians who fled to the kingdom during the 1948 Middle East war.