This was supposed to be the administration of unprecedented transparency. President Obama promised that when he took office, and the White House’s Web site says so on this very day. It reads:

My administration is committed to creating an unprecedented level of openness in government. We will work together to ensure the public trust and establish a system of transparency, public participation, and collaboration. Openness will strengthen our democracy and promote efficiency and effectiveness in government. Government should be transparent. Transparency promotes accountability and provides information for citizens about what their government is doing.

Instead, it’s turning out to be the administration of unprecedented secrecy and of unprecedented attacks on a free press. I wrote about the chilling effect of the Obama administration’s leak investigations – including the ramped-up criminal prosecution of those who provide information to the press — in a Sunday column in March.

Now that situation, already bad, has taken a major turn for the worse with revelations that the Obama Justice Department had secretly seized the phone records of a large number of journalists for The Associated Press, as part of a leak investigation.

While it may not be immediately apparent, readers have a big stake in this development.

Why should what happens to another news organization matter to Times readers?

For several reasons. Partly because the situation speaks directly to being able to know how your government operates. It’s hard to avoid sounding a little corny — all civics class and founding fathers — when talking about it: The ability of the press to report freely on its government is a cornerstone of American democracy. That ability is, by any reasonable assessment, under siege.

Reporters get their information from sources. They need to be able to protect those sources and sometimes offer them confidentiality. If they can’t be sure about that – and it looks increasingly like they can’t – the sources will dry up. And so will the information.

Sad to say, that seems to be exactly what the Justice Department has in mind with its leak investigations, two of which involve Times journalists. One has to do with the chief Washington correspondent David Sanger’s book and articles about American cyberattacks against Iran, the other is Scott Shane and Jo Becker’s article from last May about Mr. Obama’s “kill list.”

The Times’s executive editor, Jill Abramson, put it simply when I asked her about it Tuesday: “The press is supposed to hold government accountable. These investigations intrude on that process.”

The Times stories that are the subject of leak investigations “were in the great tradition of Washington reporting, helping people understand how decisions were made,” The Times’s newsroom lawyer, David McCraw, told me Tuesday. “There was no compromising of national security involved.”

“The net effect is universal,” he said. “People are less willing to talk, and that’s a loss for everyone.”

The Times is one of the many news and press rights organizations that signed a strongly worded letter sent to the Justice Department leadership on Tuesday.

This isn’t just about press rights. It’s about the right of citizens to know what their government is doing. In an atmosphere of secrecy and punishment – despite the hollow promises of transparency — that’s getting harder every day.