In a statement, the ministry condemned the Israeli measures against the holy mosque.
Israel closed Al Aqsa and banned the Friday prayer following a nearby attack that left three Palestinians and two Israeli policemen dead.
The Israeli government headed by Benjamin Netanyahu bears full and direct responsibility for its aggressive actions, illegal measures and gross violations of the status of Al Aqsa since 1967, the ministry said.
It added that the international reactions have not lived up to the required level and are not enough to pressure the occupation authorities to immediately stop their ongoing aggression.
On different occasion, Israel under heavy police presence partly reopened a Jerusalem holy site on Sunday after taking an unusual step of closing it down following a deadly shooting attack, according to the police.
Police spokeswoman Luba Samri said that "some 200 Muslim worshipers entered the site during the first 30 minutes and people are continuing to enter."
Members of Waqf, the Muslim custodians of the holy site, refused the new security checks at the site, Samri said.
On Saturday, Israel announced that the compound would be reopened after the police fortified the security measures there, including new metal detectors and CCTVs that were installed on poles and covers the entire compound.
Samri said that as a first step only residents of Jerusalem, including East Jerusalem, would be allowed. Samri said the entrance is currently allowed only through the Lions Gate, where metal detectors have already been installed. More gates are expected to be opened, she added.
On Friday morning, three Palestinian Arab citizens of Israel opened fire near the gates of the compound, killing two Israeli policemen. The gunmen were subsequently shot and killed by the police.
The shootout sparked fears of a new round of violence in the region, Xinhua reported.
The al-Aqsa mosque compound, holy to both Muslims and Jews, in one of the most sensitive sites in the region. The flashpoint site is holy to both Muslims, who revered it as the Noble Sanctuary, and to Jews, who know it the Temple Mount.