'State secrets' and 'security considerations' are often cited to conceal administrative and ethical errors from the public eye. Such is the case in the "security affair" that for weeks has stoked the public's curiosity.

At first glance, this 'affair' has to do with the transfer of classified material to Haaretz correspondent Uri Blau, the very act of which was supposedly "harmful to national security."

In reality, however, the crime in question is far more severe - the one committed by the security apparatus (GOC Central Command in particular) in ignoring a High Court order and approving the targeted assassination of wanted men who could otherwise have been detained, in strikes that claimed the lives of innocent civilians.

That is the real affair that needs to be investigated, one whose protagonists are not the Haaretz reporter - who did excellent work in exposing the system's failings to the public - or his sources, but those same senior commanders who chose to so blatantly flout the High Court ruling.

The secondary affair, the one involving alleged breaches of national security, began in September 2009 when Blau was summoned by Shin Bet agents and instructed to hand over documents he had used in preparing a number of articles.

From that moment, Haaretz was in contact with the security service's legal adviser over returning the documents, hoping to protect the reporter's sources and freedom of action without damaging national security.

Those discussions led to an agreement reached in September 2009, by which Blau provided the Shin Bet with dozens of classified documents in his possession. In return the intelligence agency pledged not to question the reporter about his sources or any other matter, and not to use the documents as evidence in a potential lawsuit over leaked information.

All of the articles in question that were printed in Haaretz were first approved by the military censor. Rather than rush to investigate the military's breach of the High Court order, the security apparatus chose only to examine the leak that spread the supposedly damaging files.

Shortly after the agreement was signed, the Shin Bet detained Anat Kam, a former soldier in the bureau of the GOC Central Command, on suspicion that she was Blau's source. In January of this year the security service announced that the reporter was also wanted for questioning, in clear violation of the agreement between the Shin Bet and Blau.

Thus the agency breached the terms it had agreed to, and later rejected a proposal to draft a new agreement that would both meet the Shin Bet's goal of protecting national security and uphold the immunity of Blau's sources.

Shin Bet's director described the documents as the kind of classified files enemy countries would be pleased to get their hands on. Maybe so. But some of those same enemy states would also be happy to see Israel conducting itself as they do, waiving the democratic principles that depend on a free press.

An investigation into the transfer of classified documents is legitimate, but cannot come in place of the inquiry that is truly called for.