WASHINGTON -- In his 2009 speech to the Muslim world, President Obama announced a new effort to eradicate polio, which persists in three Muslim countries. One of the biggest hurdles had been persuading some local leaders that vaccination campaigns were independent health efforts, not nefarious programs being run by the CIA.

With the Obama administration's assurances, Muslim scholars issued a religious decree that parents should vaccinate their children. The administration and public health officials cheered as the number of new polio cases began to fall in some hard-to-reach areas.

Recently, however, as the U.S. closed in on Usama bin Laden's compound in Pakistan, the CIA used a vaccine program as cover, a way to try to collect DNA from bin Laden's family and confirm he was hiding inside a walled compound.

Public health officials swiftly criticized the move, saying the independence of health workers must be sacrosanct. World Health Organization spokeswoman Sona Bari said health officials were caught by surprise when the story was first reported by the Guardian newspaper in London. The Associated Press has confirmed details about the vaccination program from U.S. officials.

"It's just so unfortunate. It's the worst kind of labeling you could put on a public health campaign," Bari said Wednesday. "Any backlash against this will hurt the children of Pakistan."

Polio is endemic in three Muslim countries -- Nigeria, Pakistan and Afghanistan -- but some Muslim leaders have been suspicious of vaccination efforts, suggesting they were part of a CIA sterilization campaign. Allaying those fears has been crucial to getting doctors and nurses into some areas.

The vaccination program used in the CIA's hunt for Usama bin Laden was a real one, for hepatitis.

Neither the White House nor the CIA would speak about the program. A senior U.S. official, speaking on condition of anonymity because the program remains secret, said the decision to use vaccinations as a cover was a rare move that reflected the seriousness of the hunt for bin Laden.

Intelligence officials were under pressure to confirm bin Laden was in the compound before the president risked American lives.

But the move directly contradicts the administration's own message to the Muslim world. And health experts say maintaining confidence in vaccination drives is far more important than even the hunt for bin Laden. Polio, for instance, is on the verge of eradication but remains a stubborn problem, particularly in areas such as the Afghanistan-Pakistan border, where there is great mistrust of the U.S. and where the CIA launches missile strikes on suspected terrorists from unmanned aircraft.

The expanded polio vaccination effort was seen as key success for the Obama administration's Global Engagement Directorate, which is run out of the National Security Council. Top members of the National Security Council were deeply involved in the bin Laden raid, but it's unclear whether that included the people championing the polio effort.

"I can't imagine the people involved in that effort knew about this," Bari said. "It's beyond the pale of the imagination."