In times of crisis, the White House, the Congress and the government often turn to reorganization to fix what has gone wrong. Move the boxes on the organizational chart. Draw a new schematic.

But as the 9/11 Commission report said, “We know that the quality of the people is more important than the quality of the wiring diagrams.”

Five years after the Sept. 11 attacks, the government has boldly reorganized (for better or worse, depending on your vantage point).

The 9/11 Commission’s recommendation to pay more attention to the people of government also led to bold plans.

"Questions that might have been debated earlier are starting to be asked, including what meaning to give to post-9/11 civil service reform."

In November 2002, President Bush signed legislation authorizing a new approach to paying, promoting and disciplining about 110,000 employees of the newly created Homeland Security Department. A year later, Bush signed similar legislation to overhaul pay and personnel rules for the nearly 700,000 Defense Department civil-service employees.

In 2004, Congress moved to overhaul the intelligence community—a group of 16 agencies with more than 100,000 employees. This year, talks began inside the intelligence community on how to revamp pay scales and provide interagency experience, through job rotations, for the next generation of intelligence leaders. A range of other initiatives were launched—to bring to government more linguists who understand the cultures of the Middle East and Asia, to bring back federal retirees to create an FBI cadre that could be called up on short notice, and to shake up federal pay on a governmentwide basis by abolishing the General Schedule in 2010 in favor of pay-for-performance systems mirroring changes underway at DHS and at Defense.

All in all, an amazing amount of change, or proposed change, that proponents argued would create a more nimble, agile government.

But the promise of much of this change has not been achieved. The flawed response to Hurricane Katrina undercut contentions that the government was changing its ways. Federal courts ruled that the Bush administration had overreached in writing regulations aimed at restricting union rights at DHS and Defense, slowing the rollout of the new personnel systems.

Now that DHS and Defense are in the “implementation phase,” it’s clear that the personnel management changes set in motion by 9/11 did not receive the full discussion that reform often demands. As a recent study by researchers at the Naval Postgraduate School pointed out, key decisions on DHS were made in secrecy by White House policy and budget officials.

Questions that might have been debated earlier are starting to be asked, including what meaning to give to post-9/11 civil service reform. How do federal leaders preserve “core values” and a “merit system” that protects employees from political pressure—and promote accountability through performance management systems geared to a president’s agenda?

In a recent issue of Public Administration Review, Patricia Wallace Ingraham, a Syracuse University scholar, argued that the government’s strong emphasis on performance in recent years “forces reconsideration of the idea of merit and civil service as synonymous.”

She wrote that “performance on the job becomes as critical as qualifications for the job,” and salutes the effort to change personnel rules at DHS and Defense. Performing one’s job to the best of one’s ability and performance in pursuit of an agency’s mission “are strong links to merit,” she said. She concluded that the current civil-service structures and procedures “are not providing merit a happy home.”

But James R. Thompson, a University of Illinois professor writing in the same issue of Public Administration Review, came to a different conclusion. He sees the civil service as “an institution in the process of being deinstitutionalized.”

In Thompson’s view, reforms based on pay-for-performance systems give managers greater control over subordinates and make the consequences of disagreements much more severe for employees. Such pay systems exacerbate the tension between enhancing performance and acting pursuant to a public service ethic, he wrote.

“Public service implies working in the public interest even, and especially, when one is subject to pressures to do otherwise,” Thompson said.

He concluded that the new personnel systems at DHS and Defense pose “the most immediate threat to the federal civil service” and asserted that the systems “are being implemented in an environment that is overtly hostile to merit ideals.”

The debate has been joined, at last, and that is important. As Linda M. Springer, the president’s chief civil-service adviser, told a Senate committee, “After all, it’s the people in government who make government work.”

Stephen Barr writes the Federal Diary column at the Washington Post and hosts a weekly discussion on washingtonpost.com.