The synagogue was renovated from funds donated by Jewish-American millionaire Erwin Moskowitz, who made headlines recently due to his involvement in a construction project in the east Jerusalem neighborhood of Sheikh Jarrah, where he plans to build 22 housing units for Jewish residents.
The Sheikh Jarrah project sparked a row worldwide, with the United States, Russia, France and many other countries condemning Israel's plan to build in the area.
Barak arrived at the synagogue ceremony on the backdrop of harsh protest and pressure by the international community against the government's legitimization for the housing of Jews in the eastern part of the city.
An official at Barak's office rejected the claims, saying that "the defense minister does not have to apologize for taking part in a ceremony welcoming a new Scroll of the Torah at a synagogue which has existed since 1867."
The official said that the defense minister took part in a ceremony at a synagogue located in the Western Wall and that "the Torah scroll was donated by friends of the Association for the Wellbeing of Israel's Soldiers in the United states."
The synagogue building is sponsored by Western Wall Rabbi Shmuel Rabinovich, but is physically located within the Muslim Quarter.
The synagogue in question was inaugurated last September, after being renovated and reconstructed with a donation from Moskowitz, who helps Religious Zionism associations buy houses and buildings in Jerusalem neighborhoods where the population is mostly comprised of Arab residents.
Minister Barak said during the ceremony, "We are now several days after Tisha B'Av and remember very well why the First Temple was ruined and why the Second Temple was ruined, also because of unfounded hatred.
"We should implement the lessons of those days at that time. We bear the responsibility in our country and for the State of Israel's security and for the security of Jews' lives anywhere in the world and we must always remember that despite all the disagreements between us, we are all brothers. We have the land, the security and the knowledge that we are brothers."
'The minister need not apologize'
The defense minister's office said in response to Ynet's inquiry, "Not one of us had an idea that the synagogue is not part of the Western Wall compound. We had no idea that Moskowitz is one of the benefactors of the synagogue renovations.
"The Torah scroll that was brought there was a donation from the Falik family, a friend of the Association for the Wellbeing of Israel's Soldiers. The defense minister need not apologize for attending a ceremony for introducing a new Torah scroll to a synagogue, which was established by Jews already 142 years ago."
The area of the Western Wall complex, next to which is the said synagogue, has in recent years been at the heart of another controversy. Israel plans on building a new bridge over Mugrabi Gate. Prime Minister Netanyahu recently rejected these plans out of concern that decisions made on the eve of the Ramadan holiday could ignite Jerusalem streets and cause an international outcry.
Another example of the flammable state of affairs in east Jerusalem took place Saturday night when a number of National Union Knesset members toured the Sheikh Jarrah neighborhood, causing clashes to break out between Arab and Jewish residents there. Five people were arrested on suspicion of throwing stones. Two others were detained for investigation under suspicion that they endangered lives on a major thoroughfare. No injuries or damage were reported in the incident.
Efrat Weiss contributed to this report