Barak said the comments, made by Defense Ministry official Amos Gilad, do not reflect Israel's position. Barak also said that Gilad's words came after he spoke at length about the importance of the peace treaty and proper relations between Israel and Egypt.
Gilad was speaking Friday to students in the city of Herzliya. The remarks were widely reported by Israeli media.
"There has been a tremendous historic change in Egypt with the rise of the Muslim Brotherhood," Gilad said.
"We do not exist as far as they are concerned. There is no dialogue on the high political level between us with this president, and I don't think there will be in my opinion. Out of desire for democracy has grown a shocking dictatorship. Where are all the young people who demonstrated in Tahrir square? They have disappeared," Gilad said.
Israel's relations with Egypt have been strained since the ouster of longtime President Hosni Mubarak in a popular uprising last year. His successor, Mohammed Morsi, hails from the Muslim Brotherhood.
Israel has refrained from criticizing Morsi's government, and Gilad's comments were rare.
The peace agreement with Egypt is critical to Israeli security, and Israel's leaders do not want to damage the already strained relationship.