WHEN THE Justice Department launched its investigation of alleged leaks of national security information by the Obama administration a year ago, we were skeptical. The history of such probes is mainly a tale of dead ends and unintended negative consequences. That this effort to criminalize a leak was launched amid an election-year uproar seemed especially inauspicious.

Our forebodings have been borne out with the revelation that federal prosecutors have undertaken a broad sweep of the Associated Press’s phone records. Whatever national-security enhancement this was intended to achieve seems likely to be outweighed by the damage to press freedom and governmental transparency.

The Justice Department’s apparent purpose is to track down the person or persons who told AP about the Central Intelligence Agency’s disruption of a Yemen-based terrorism plot. Federal prosecutors subpoenaed records for 20 separate office, home and cellular phone lines belonging to the AP and its reporters or editors. The subpoenas covered a two-month period in the first half of 2012. Crucially, they did not follow the usual Justice Department policy, which is to give news organizations a chance to negotiate or contest such a subpoena ahead of time.

That policy is rooted in sound respect for the First Amendment. It’s not legally binding — in part because the Justice Department and the press have recognized a mutual interest in resolving such matters without potentially counterproductive Congressional or judicial intervention.

In a letter to AP President and CEO Gary B. Pruitt yesterday, Deputy Attorney General James M. Cole explained that the department had no alternative means of gathering essential information. He also intimated that Justice had kept AP in the dark until a few days ago so as to avoid “a substantial threat to the integrity of the investigation.” Attorney General Eric H. Holder Jr., who recused himself from the investigation after he was interviewed by the FBI, fleshed that assertion out at a press conference Tuesday, saying at issue is one of “the top two or three most serious leaks that I have ever seen” which “put the American people at risk, and that is not hyperbole.”

Perhaps that’s so — we have no independent means of verifying Mr. Holder’s claim, though we hope reporters are working on it. As Mr. Pruitt responded Tuesday, “We held that story until the government assured us that the national security concerns had passed. Indeed, the White House was preparing to publicly announce that the bomb plot had been foiled.”The usual reason for keeping a subpoena secret is that the target would otherwise try to destroy documents. In this case, AP could not have done so even if it wanted to, since the relevant records were in the possession of its phone service providers. Without even giving AP a chance to weigh in, we don’t see how the department could intelligently weigh its prosecutorial needs against this broad subpoena’s chilling effect on reporters and their sources

Of course, if Justice Department officials are overreacting, they aren’t alone. The investigation of AP began in response to Republican outrage about the purported fact that White House officials were leaking secret information and spinning it to make President Obama look good for reelection purposes. In response, the Obama administration launched the present investigation, on top of the six (mostly unsuccessful) ones it had attempted previously — which, judging on costs and benefits visible to date, was probably six too many.