The country's National Security Council (or, more properly, the National Security Staff), headed by a National Security Advisor (NSA), was created as a way to mitigate these pathologies. First established in 1999, it was given concrete form and legal standing with the 2008 National Security Law. A body composed of representatives of different ministries and agencies, the NSC is supposed to provide an array of options -- as opposed to specific recommendations -- regarding both the general security situations and specific developments as they crop up. It is, as Chuck Freilich has suggested, the best hope for making decision-making more structured, formal, and effective.
Unfortunately, longstanding patterns of decision-making, based on Israel's history, threat environment, and politics, have proved difficult to change. Israeli security decision-making is informal, secret (though sometimes punctured by leaks), and typically dependent on only a few individuals, particularly at the strategic level (tactical and operational decisions coming out of the security establishment tend to be more formal and systematic).
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