In his last public appearance as head of the VA, former Veterans Affairs secretary Eric K. Shinseki gives a speech to a coalition concerned about homeless veterans on Friday morning. Later Friday morning, President Obama announced that Shinseki had resigned after five years on the job. (Nikki Kahn/The Washington Post)

It was a lie, of course. But it seemed to be a very important lie, one that the system depended on. “Two to three times a month, you would hear something about it,” Turner said — another reminder from supervisors to “zero out.” “It wasn’t a secret at all.”

But all this was apparently a secret to Secretary Eric K. Shinseki, perched 12 levels above Turner in the VA’s towering bureaucracy. Somewhere underneath Shinseki — among the undersecretaries and deputy undersecretaries and bosses and sub-bosses — the fact that clerks were cheating the system was lost.

On Friday, Shinseki resigned and was replaced by his deputy.

But his departure is unlikely to solve the VA’s broader problem — a bureaucracy that had been taught, over time, to hide its problems from Washington. Indeed, as President Obama said, one of the agency’s key failings was that bad news did not reach Shinseki’s level at all.

This is an ironic development: Until recently, the VA had been seen as a Washington success story. In the 1990s, reformers had cut back on its middle management and started using performance data so managers at the top could keep abreast of problems at the bottom.

Then that success began to unravel.

As the VA’s caseload increased during two wars, the agency grew thick around the middle again. And then, when the people at the bottom started sending in fiction, the people at the top took it as fact.

“Shinseki goes up to Capitol Hill, and says, ‘I didn’t know anything.’ I find it perfectly believable,” said Paul C. Light, a professor at New York University who has studied the bureaucracy of the VA and others in Washington. “And that’s a real problem.”