Among the most telling aspects of the state comptroller’s report, published Wednesday, which chronicles a slapdash decision-making process inside the Prime Minister's Office in general, and with regard to the Mavi Marmara incident in particular, was Prime Minister Binyamin Netanyahu’s official response to it.

In the final analysis, Netanyahu said in a statement issued by his office, "Israel's citizens are enjoying a level of security that they have not known for years.”

In other words, forget all Comptroller Micha Lindenstrauss’s carping about shoddy preparation, about a decision-making process dominated by the defense establishment, about the lack of input from the security cabinet on key and vital issues; The only thing that really matters are the results. And the overall result of the last three years is a security situation for Israelis that is better than it has been in recent memory.

This good security situation didn’t just appear out of the blue, the PMO response continued. Rather, “this security is the direct result of responsible management and determined policy. The security discussions that have been held over the past three years have been unprecedented in their scope and depth, as attested to by those who have participated in them.”

That last line has been the PMO and the Defense Ministry’s mantra whenever they are criticized about how decisions are made – whether the criticism comes from the comptroller, the former head of the Mossad or the former head of the Shin Bet.

But the comptroller’s report showed that not all the participants in these discussions were thrilled about how they were handled. In fact, some of those who participated in discussions over the Mavi Marmara – like Strategic Affairs Minister Moshe Ya’alon, for instance – were less than impressed by their scope and depth, and instead complained to the comptroller that these meetings were not exhaustive at all.

The report that Lindenstrauss released Wednesday – dealing with the implementation (or lack of implementation) of the 2008 National Security Council Act that established the National Security Council; the decision-making process that preceded the boarding of the Mavi Marmara; and the public diplomacy handling of the incident – is not an easy read, and not only because it extends over 153 pages of dry, repetitive, bureaucratic prose.

It is an uncomfortable read because, as the nation sits on the cusp of critical decisions that will need to be taken regarding Iran, this report paints a picture of a national security and foreign policy apparatus very much in the grips of the defense establishment, where preparatory work is not properly carried out, where orderly meetings are not conducted on a regular basis, and where information is compartmentalized and concentrated – again – in the hands of the defense establishment.

Have you ever heard of Yohanan Locker? You should have, because if the comptroller is correct, this man – who serves as Netanyahu’s military liason – is one of the most influential men in the country.

Despite the National Security Council Act of 2008 that legislated that the head of the National Security Council would be the prime minister’s chief national security adviser, in practice it is the military liaison.

The problem with this arrangement is twofold. First because the military liaison does not have the proper staff or expertise to coordinate the prime minister’s meetings on national security issues, and secondly because he is part of the defense establishment. If the military liaison is the one preparing key national security meetings, raising the issues to be brought to those meetings and both providing the intelligence information and determining who can see it, then one perspective has a leg up on all the competition – that of the defense establishment.

This arrangement, Lindenstrauss concluded in his report, is not healthy, and in fact runs contrary to the National Security Council law. Yet Netanyahu, he said, has not stepped in and foisted the National Security Council on the decision-making process, as he should have done.

Netanyahu’s response to this, as contained in the 200-word response on this matter issued by his office, was simple: The proof is in the pudding, and the pudding – at least the security aspect of the pudding – tastes good.

Except that when it came to the Mavi Marmara, the pudding was not good; It was bitter indeed.

To which the PMO replied that the Mavi Marmara was a different case, and that even the comptroller himself had written in the report that he was not convinced that had the decision-making process been different leading up to the May 2010 flotilla, the results would have been different.

In other words, the PMO is saying that even had they followed all the rules and regulations laid down in the National Security Council act of 2008, which regulates the bureaucratic processes that needs to go into making weighty decisions, there was no guarantee that the results would have been any different.

While that indeed may be true, it misses a key point that the comptroller was stressing: process, method and procedure are vital.

High-quality process, proper procedure and good method in decision-making do not guarantee success, but they may increase the chances of success and limit the probability of failure. Of course results are important, but good process leads to a greater likelihood of good results.

And what Lindenstrauss pointed out was that the process before the Mavi Marmara was faulty.

True, that’s is not why nine Turks who clashed with IDF soldiers on a ship hell-bent on provoking Israel and bashing the blockade of Gaza were killed in May 2010 and that’s not why key strategic relations with Turkey have gone down the drain. But a better decisionmaking process – bringing everyone into the picture together and in an orderly, systematic fashion – might have enabled Israel to deal with the flotilla better.

And, as Lindenstrauss pointed out, the flotilla is a metaphor; a metaphor for a type of decision-making process that, while improving, is not what it should be – especially considering the life-and-death decisions that those at the top of Israel’s pyramid are entrusted to make.

One central theme emerged throughout the report: process matters, because process shapes substance.

If you plan as necessary, and in this case as determined by the National Security Council law of 2008; if you involve everyone who has to contribute; if you do the necessary staff work that includes objectively comparing and evaluating all the options; if you are systematic in preparatory work that goes into high-level meetings; if you work on an inter-agency level; if the staff-work is done by the best and the brightest and the product produced is rigorous and exhaustive; then the likelihood of error because of insufficient planning, or not taking something into consideration, is lessened.

Procedure can’t guarantee success, but – at least according to the comptroller – it is a necessary condition for it. Proper process is not sufficient for success and ultimately resolves on the wisdom of those who make the decisions and implement them, but proper procedure can ensure that the leaders are equipped with everything they need when approaching those decisions.

And that, Lindenstrauss made clear, was not the case in the run-up to the Mavi Marmara, and it is systemically not the case at the highest level.

Wednesday's report did not come in a vacuum.

Indeed, it should be seen as an extension of various committees of inquiry and comptroller documents stretching back numerous years.

One of the frustrating things about reading the report was that it contained so many echoes of the Winograd Commission report from 2008 that criticized the decision-making process in the run-up to and during the Second Lebanon War, and the subsequent Lipkin-Shahak committee report that was mandated with providing recommendations for implementing the Winograd Commission findings. One of the Lipkin-Shahak committee’s key recommendations was to strengthen the National Security Council.

To say that nothing has changed would be unfair. Things have changed. For instance, the National Security Council, the body now empowered by law with being the prime minister’s main advisory body on national security issues, is much more active than it was during the Second Lebanon War, or when Netanyahu and his then-foreign policy adviser Uzi Arad pushed the idea in 1999.

Indeed, Arad – who was fired from his position as head of the National Security Council in 2011 amid allegations that he leaked sensitive information – has reason today to feel doubly vindicated.

His first vindication, a personal one, came in March, when then-deputy attorney-general Raz Nizri said in a Knesset committee meeting that Arad had not leaked sensitive material.

And his second vindication, a professional one, came with Wednesday’s publication of the comptroller’s report, since his twoyear tenure inside the PMO was marked by a fierce turf battle with the prime minister’s military liaison. The comptroller sided with Arad, saying with no equivocation that the National Security Council, not the military liaison, is the prime foreign policy advisory body inside the PMO and should be the body in charge of coordinating, preparing and taking part in the key meetings on national security issues.

For years that was not the case; for years the defense establishment held sway, and it is only natural that it will not relinquish that prerogative readily. Nevertheless, Lindenstrauss concluded that it must do so for the sake of proper procedure and process.

And if it does not do so willingly, he wrote, then the prime minister must force it to do so.

Otherwise? Well, otherwise – as Lindenstrauss wrote in a phrase that summed up his whole report – “the flotilla is a metaphor.”