"It was barbaric, impudent," a foreign ministry spokesman, Hassan Kabia, told AFP.
He would not identify the visitors but described them as "social activists, bloggers and media people."
Jerusalem and its holy sites are the most sensitive issues in the Israeli-Palestinian conflict.
The Al-Aqsa mosque compound is the third-holiest site in Islam.
Jews refer to it as the Temple Mount, revered as the location of the two biblical-era temples, and consider it their holiest place.
It is located in east Jerusalem, occupied by Israel in the 1967 Six-Day War and later annexed in a move never recognised by the international community.
The visit comes as Israel seeks to improve ties with Gulf Arab countries, with which it has no formal diplomatic relations.
Those states have held off offering Israel formal recognition due to its continuing occupation of Palestinian territory, but their relations have warmed of late, largely due to common concerns over Iran.
The journalists were to visit Jerusalem's Yad Vashem Holocaust memorial, parliament and holy sites, among others, the foreign ministry said in a statement.
It said it had "the aim of exposing the journalists some of whom come from countries that do not have diplomatic relations with Israel to Israeli positions on diplomatic and geopolitical issues".
Jordan is also participating, the ministry said.
It is one of only two Arab countries, along with Egypt, that has diplomatic relations with Israel.
On Thursday, Israeli foreign minister Israel Katz said he had met his Bahraini counterpart publicly for the first time during a visit to Washington last week.
Katz also recently visited Abu Dhabi for a UN climate conference, where he met United Nations chief Antonio Guterres and an unnamed "high ranking UAE official".
The Saudi visitor, named by Israeli public radio as Mohammed Saud, was one of six invitees from Arab states brought to Israel by its foreign ministry to give them fresh viewpoints on the country.