Palestinians from Gaza pray in front of the Dome of the Rock during their visit at the compound known to Muslims as Noble Sanctuary and to Jews as Temple Mount in Jerusalem's Old City October 5, 2014
Temple Mount, the home of Al-Aqsa Mosque, is a frequent site for violent clashes between Palestinians and Israeli forces.REUTERS/Ammar Awad

Israel's chief military rabbi claimed that the religious significance of a contested Jerusalem compound to Islam is an invention, as an overwhelming majority of Muslims have no idea what's actually written in Quran.

In comments that are likely to further exacerbate tensions in the Holy City, Israel Defence Forces (IDF) Brig. Gen. Rafi Peretz claimed Muslims have no real reason to pray at Temple Mount, known as al-Haram al-Sharif in Arabic (The Noble Sanctuary).

The IDF has apologised for the remarks, which it says were taken out of context.

"Jerusalem isn't mentioned in the Koran even once. Not even in a hint. The Arabs are imagining things," Peretz said during a lecture at pre-Military Academy in Moshav Nave in November.

A video of the address was published on the website Kipa this week.

"90% of the Arabs don't know a thing about the Quran. I tell you with full authority. We know better than many of them," Peretz said, according to a translation by Haaretz newspaper.

Temple Mount has been a flashpoint of tensions between Muslims and Jews in recent weeks, over proposed plans to enhance Jewish access to the site.

Sitting just above the Western Wall, the compound comprises the iconic Al-Aqsa Mosque and the Dome of the Rock.

The Mount is Islam's third holiest site after Mecca and Medina as it is considered to be the place where Muhammad ascended to heaven.

Rafi Peretz
IDF chief rabbi Rafi Peretz claimed Muslims have no real reason to pray at al-Haram al-Sharif in Jerusalem.YouTube

"The only mosque any holiness is attributed to is Al-Aqsa. The rest of the Temple Mount has no religious significance," Peretz claimed.

"When [Muslim worshippers] bow, they bow to Mecca but their backside is turned to the Temple Mount," he added. "So what are they doing on the Temple Mount?"

The compound is also the holiest site for Jews that believe it is the place where God chose the Divine Presence to rest.

The chief rabbinate has always opposed Jewish worship there, because, according to traditional Orthodox Judaism, Jews entering the area might stumble upon and profane the "Holy of Holies," or the inner sanctum of the Second Temple that was destroyed by Romans in 70 AD.

Nevertheless some hard-line Jewish activists have been demanding they are allowed to pray there - something they are currently banned from doing.

The site has been administered by an Islamic Waqf (trust), under the authority of Jordan, since the crusades, while Israel has controlled access to it since the occupation of East Jerusalem in 1967.

Israeli authorities have implemented a ban on all non-Muslim prayers as a security measure.

Jewish claims to the compound are one of the most thorny and sensitive political issues on the backdrop of the Arab-Israeli conflict.

Yehuda Glick a vocal Israeli campaigner for greater Jewish access to Temple Mount was shot and wounded in October, allegedly by a Palestinian gunman.

An IDF spokesman told the Times of Israel newspaper that Peretz's comments "were taken out of context and do not reflect the position of the IDF chief rabbi. The rabbi is sorry if his remarks offended the Arab population."