"This is an attempt to change the current historic and legal status of Al-Aqsa Mosque... a provocation to the feelings of Muslims and a clear violation of relative international resolutions," the ministry said in a statement.
The ministry held Israel responsible for the "repercussions of the continuation of such daily violations on Jerusalem."
"The ministry reiterates Libya’s position towards the justice of the Palestinian cause and calls on the international community to live up to its responsibilities and end those Israeli violations, which could fuel conflict, extremism, and instability in the region," the statement added.
On Tuesday, Ben-Gvir made a visit to the flashpoint holy site of Al-Aqsa Mosque compound in East Jerusalem, triggering a furious backlash from the Muslim world in the Middle East.
The Al-Aqsa Mosque compound, known to Jews as the most sacred site, is regarded by Muslims as their third-holiest site.
The holy site has been administered by the Jerusalem Islamic Waqf, a Jordanian body, since 1948. Under a 1967 agreement between Israel and Jordan, non-Muslim worshippers can visit the compound but are prohibited from praying there.