The Defense Ministry on Monday attempted to soften its statement from last Friday comparing the Iran nuclear deal with Hitler's 1938 Munich pact.
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Last week's unusual statement was issued in response to a remark by United States President Barack Obama that even the Israeli military establishment agreed that the outcome of the Iran agreement had been positive.
Prime Minister Benjamin Netanyahu quickly distanced himself from the statement. A senior aide to the prime minister had informed U.S. Ambassador to Israel Dan Shapiro that Netanyahu only learned about it from the media.
On Monday, the Defense Ministry said it was issuing a new statement "in light of the mistaken significance given by the media to the statement by the defense apparatus last Friday that referred to the Munich pact."
It said that it had not intended to make a direct comparison with the Holocaust.
"Friday's statement was not intended to make a direct comparison, either historically or personally," Monday's statement said. "We are sorry if it was understood otherwise."
The ministry stressed the cooperation between Israel and the U.S. in its new statement.
"The differences between the position of Israel and that of the U.S. on the issue in no way impair our deep appreciation of the U.S. and the American president for their huge contribution to the national security of Israel and the enormous importance that we attribute to the robust partnership between the two countries."
The ministry also acknowledged indirectly that Iran is currently abiding by the terms of the agreement it signed with the United States and other world powers.
"Israel remains deeply concerned that even after the agreement, the leadership of Iran continues to declare that its central goal is the destruction of the State of Israel and continues to threaten the existence of Israel in word and deed.
"Even if Iran abides by the nuclear agreement, its stated and official policy to work for the destruction of Israel denies its legitimacy in the international community."
On Friday, the ministry said that "agreements are of value only if they are based on the current reality, and they have no value if the facts on the ground are entirely contrary to those on which the agreement is based."