Jordan's Foreign Ministry said Israeli authorities had “intercepted” the Jordanian ambassador to Israel as he entered Al Aqsa Mosque in Jerusalem on Tuesday.
The ministry said an Israeli policeman “blocked the way of the Jordanian ambassador [Ghassan Majali] as he entered the blessed Al Aqsa Mosque”.
Israel's ambassador in Amman, Eitan Surkiswas, was summoned to the ministry, where the Jordanian government affirmed its “condemnation of unacceptable interference in the affairs of Al Aqsa”.
The incident occurred as Jordan’s King Abdullah and Palestinian leader Mahmoud Abbas flew to Cairo for a meeting with President Abdel Fattah El Sisi, during which Israel's new far-right government will be discussed.
Haaretz quoted witnesses as saying that Israeli police at the compound had either asked Mr Majali to co-ordinate with Israeli authorities before he entered or that he was allowed to enter after he was identified as the Jordanian ambassador.
He eventually left, the paper said.
The mosque is one of Islam's holiest sites. Jordan claims custodianship over Al Aqsa and other holy sites in the Old City, which was captured by Israel in the 1967 war.
The 1994 peace treaty between Jordan and Israel says the country respects a “special role” for Jordan in Muslim sites in Jerusalem, but does not directly endorse the kingdom’s claims of custodianship.
Earlier this month, Jordan condemned a visit by hardline Israeli minister Itamar Ben-Gvir to Al Aqsa Mosque compound, calling it a breach of international law.
A photograph of Mr Ben-Gvir, Israel's new National Security Minister, at the site has raised tension between Israel and the Palestinians, days after the swearing-in of a far-right government led by veteran politician Benjamin Netanyahu.