Two decades after the Sept. 11 attacks, there are again dozens of unfilled Senate-confirmed national security positions.,

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WASHINGTON — Before the Sept. 11, 2001, terrorist attacks, nearly half of the federal government’s Senate-confirmed top national security jobs sat empty, making the United States more vulnerable, the 9/11 Commission found. Two decades later, the situation — by at least one measure — is worse.

Only 26 percent of President Biden’s choices for critical Senate-confirmed national security posts have been filled, according to a new analysis by the Partnership for Public Service, which aids presidential transitions and tracks appointments. Immediately before the 2001 attacks, 57 percent of key national security positions were occupied.

“What appalled the 9/11 Commission has gotten dramatically worse,” said Max Stier, the organization’s chief executive. “The Senate confirmation system is not working. It’s designed for an era of simplicity and bipartisan cooperation, which we don’t have.”

Empty seats dot the federal government’s top tier. Of 1,200 Senate-confirmed jobs across the government tracked by the group, 144 of 442 nominations submitted had been filled by the August congressional recess.

Within those 1,200 Senate-confirmed positions are 170 national security-related posts in the departments of Homeland Security, Defense, State, and Justice. Of those, only 44, or 26 percent, have been filled.

To be sure, the universe of security-related positions is far more expansive than it was in 2001, when there was no Department of Homeland Security and few officials were focused on cybersecurity or infrastructure security. There have been other changes in the 20 years since, including a network of counterterrorism centers across the country and major advances in technology that allow the intelligence agencies to track terrorists around the globe in real time.

The Partnership analysis looked only at Senate-confirmed positions, which account for a small fraction of key national security jobs. More than 70,000 positions in the intelligence agencies and more than 200,000 in the Department of Homeland Security, for example, are not subject to confirmation.

But White House officials said on Friday that clearing the logjam was critical to national security and the nation’s foreign policy and urged the Senate to move forward.

Bipartisan Stalling

To limit the nation’s vulnerability during the period between outgoing and incoming administrations, the 9/11 Commission sought to speed the transition, in part by recommending that a president-elect nominate a full slate of national security leaders no later than Inauguration Day.

Not only has that not happened, Senate logjams and partisan battles over nominees have gotten worse. It now takes nearly four months for a presidential nominee to be confirmed, compared with half that time in the Reagan era. More than 200 Biden nominees are languishing in “confirmation purgatory,” some of them for months, Mr. Stier said.

The problems started in January, when, amid a surge in domestic terrorism, Senator Josh Hawley, Republican of Missouri, slowed confirmation of Homeland Security Secretary Alejandro N. Mayorkas, saying he had questions about his stance on immigration. At the time, Michael Chertoff, a homeland security secretary during the George W. Bush administration, called the slow-walking “irresponsible and unconscionable,” saying it could “put the lives of Americans in jeopardy.”

This spring, Senator Rick Scott, Republican of Florida, slowed the confirmation of three Department of Homeland Security nominees — the deputy secretary, the under secretary for strategy, policy and plans and the general counsel — seeking greater administration attention on the U.S. border with Mexico. The deputy secretary, John K. Tien, has been on the job for less than two months, and Robert Silvers, the under secretary for strategy, for less than a month.

In August, the Senate left for its monthlong summer break with nearly 30 State Department nominees in limbo. Senator Ted Cruz, Republican of Texas, is blocking their confirmation votes while demanding that Mr. Biden impose sanctions on the Nord Stream 2 natural gas pipeline linking Russia and Germany. Among the nominees that Mr. Cruz has bottled up is Brett M. Holmgren, who was nominated in March as assistant secretary of state for intelligence and research.

But it is not only Republicans slowing the process.

Democrats grouse that liberal members of their party balk at nominees with corporate backgrounds, making acceptable appointees harder to find. Moderate Democrats have also raised objections about some nominees.

On Thursday, Mr. Biden withdrew his nomination of David Chipman to lead the Bureau of Alcohol, Tobacco, Firearms and Explosives after Senator Angus King, a Maine independent who caucuses with the Democrats, and Senator Joe Manchin III, Democrat of West Virginia, joined Republicans in objecting to Mr. Chipman’s past statements supporting some gun control.

Jamie S. Gorelick, who served on the 9/11 Commission, called the Senate’s approach “lackadaisical” and “dangerous.” During the Clinton administration, Ms. Gorelick was the Pentagon’s general counsel, and later the deputy attorney general. Then too, “it was hand-to-hand combat getting individual assistant secretaries and the like confirmed,” she said.

“I was not surprised that by September of 2001 we had a similar situation, and I’m not surprised now.”

The Biden administration, however, took office with nearly a full National Security Council staff — key posts in the White House — which was a vast improvement over the Trump administration.

But Mr. Biden has been late on some Senate-confirmed national security picks. He nominated Celeste Wallander to be assistant secretary of defense for international security affairs in late June, and last month he named Melissa Dalton to be assistant secretary of defense for homeland security and global security affairs. Both picks still await confirmation.

At the Homeland Security Department, Mr. Biden has not yet nominated anyone for under secretary for intelligence and analysis or for under secretary for science and technology.

‘Our Enemies Don’t Wait’

In September 2001, the 2000 election recount battle had slowed the presidential transition, and bitter partisan fights over some nominees delayed filling the government.

Mr. Chertoff, who was leading the Department of Justice’s criminal division on Sept. 11 and would later become homeland security secretary, recalled officials doing “double and triple duty” to cover the vacancies.

After the attacks, “the clear sense we got, and it was reaffirmed by the 9/11 Commission, is that it is a security risk not to have the process go right away,” Mr. Chertoff said in November. “Our enemies don’t wait until we’ve had a year to settle in.”

Currently more than half of the 17 top Senate-confirmed jobs at the Department of Homeland Security remain vacant. The department was abysmally understaffed during the Trump administration, complicating the pandemic response. Some top jobs have sat vacant for years because Mr. Trump failed to appoint anyone.

“The absence of confirmed positions has made it very difficult for the agency to carry out its mission,” Mr. Chertoff said.

Government watchdogs have for years recommended trimming the number of positions subject to Senate confirmation. The Presidential Appointment Efficiency and Streamlining Act of 2011 converted 163 Senate-confirmed positions to direct presidential appointments. But the numbers have been creeping upward since, from 1,212 in 2012 to 1,237 in 2016.

Elsewhere in the government, according to the Partnership for Public Service’s appointments tracker, an array of other nerve-center agencies function with acting leaders, including the Food and Drug Administration, the Federal Communications Commission and the Office of Management and Budget.

“Every department has some significant missing individuals,” Mr. Stier said. “There’s no agency where you could say ‘we’re all fine and good.'”

Eileen Sullivan, David E. Sanger, Zolan Kanno-Youngs, Alan Rappeport and Eric Schmitt contributed reporting.