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While career employees temporarily fill some of the vacancies, there's concern that the president doesn't have enough of his own people in place to advance his ambitious agenda.
"It's just not a healthy thing to have a large number of vacancies in a particularly uncertain time," said Paul Light, a professor at New York University and expert on government bureaucracy. "It should concern us."
Political appointees are nominated by the president and typically leave their posts when a new administration takes office. Career employees fill lower-ranking jobs and their tenure is unaffected by who's in the White House.
By the end of August, Obama had nominated 243 people to the 385 high-ranking policymaking jobs at the Cabinet departments that require Senate confirmation, according to the White House Transition Project. The Senate has confirmed 193 of them.
That's tracks with where Obama's predecessors were at this point in their administrations, said Terry Sullivan, executive director of the Washington-based, independent nonpartisan program that follows presidential appointments.
Obama's predecessor, George W. Bush, had 55 percent in place, though he had about 50 fewer jobs to fill.
The White House prefers to slice it a little differently to get themselves an even better grade.
The Obama White House says that by adding positions such as ambassadors and judges, who also require Senate confirmation, as well as lower-level political appointees that don't, the administration is filling jobs 50 percent faster than any of the previous three presidents at the same stage in their administrations.
The project doesn't track that list, and without Senate confirmation there is no way to follow them through votes in the Congressional Record.
Regardless of the Obama administration's overall success, however, the high-level vacancies at Treasury and HHS are particularly striking.
Obama has made improving the economy and overhauling health care the defining issues of his early presidency.
Treasury oversees the $787 billion financial stimulus; a bank bailout program and other emergency response efforts; a legislative push to overhaul financial regulation; and the government's coordination with other nations on the global economic crisis.
HHS is a nerve center for the government's response and preparation for swine flu, which could infect up to half of the U.S. population this year. Top officials are deeply involved in negotiations with Congress on health care and would have much of the responsibility of putting in place anything that gets passed.
The White House has moved some policymaking jobs into the White House, appointing at least two dozen "czars" who take on the work of advancing the president's agenda, but don't require Senate approval. At least nine focus on domestic policy, including Nancy-Ann DeParle on health care and Paul Volcker on the economy.
Light says this doesn't necessarily get the job done. These officials are focused on forming policy. Turning it into reality falls to the political appointees.
A similar rate of vacancies at a private company would be troubling, Sullivan said. But the government is "its own galaxy," he said. "You can't make a comparison to anything else in the world."
The White House puts some of the blame on the slow Senate confirmation process. In addition to the appointees already in place, seven HHS nominees and three Treasury nominees are awaiting confirmation.
But the White House has added to the hurdles.
Tax problems forced former Senate Majority Leader Tom Daschle to step aside as Obama's nominee to be health secretary. And there were other high-profile withdrawals. That led the administration to impose tougher ethics standards on their choices.
Stepping up the background checks has resulted in no more unpleasant mistakes, but has meant frustration.
Speaking last month to employees at the U.S. Agency for International Development, which is without an administrator, Secretary of State Hillary Clinton called the process "ridiculous."
"The clearance and vetting process is a nightmare and it takes far longer than any of us would want to see," Clinton said. "It is frustrating beyond words."
