A child's fingernail is marked after he received polio drops July 18 outside a bus terminal in Peshawar, Pakistan. (Karin Brulliard/THE WASHINGTON POST)

Pakistan finished its latest three-day anti-polio campaign Wednesday, deploying thousands of health workers across a nation where officials say militancy, a massive migrant population and fears about vaccines have kept the crippling virus alive.

But this round of outreach was also shadowed by a new, U.S.-made complication: revelations that the CIA sponsored a vaccination program to try to collect DNA from Osama bin Laden’s family members before U.S. commandos killed the al-Qaeda leader at a compound in northern Pakistan in May.

News of that anti-hepatitis campaign, which U.S. officials said did not succeed in collecting bin Laden DNA, has stirred outrage among international public-health organizations, which say it could deal a stiff blow to efforts to stem polio and expand routine vaccinations in Pakistan and beyond. In a nation swirling with rumors of CIA plots, critics say, this real-life one could cement public suspicions, play to radical clerics’ anti-vaccine propaganda and endanger health workers.

“This is an example of the abuse of medical care for political or military ends,” said Benoit de Gryse, Doctors Without Borders’ head of mission in Pakistan, adding that it could cause patients to view health-care providers “as potential suspects.”

Some religious leaders and Taliban militants warn that vaccines are actually American-sponsored cocktails meant to sterilize or exterminate Muslims or that Islam forbids them. Newspapers occasionally print alarmist news reports — false, health officials here say — about children who become ill from vaccines.

In 2007, as the Taliban insurgency gained strength, health officials warned that extremist clerics’ scare-mongering was driving a dramatic increase in polio cases, particularly in the religiously conservative northwest. Forty cases were reported that year; in 2010, there were 144, according to the World Health Organization.

Government campaigns have since defused, but not fully dispelled, misinformation. Maulvi Faqir Mohammed, a top Pakistani Taliban commander whose illegal radio station streams from eastern Afghanistan into northwest Pakistan, recently told listeners that vaccines are made of “extracts from bones and fat of an animal prohibited by God — the pig,” according to the Associated Press.

“In the mountains, the religious people can use it to say, ‘See? We have been saying there is an agenda,’ ” Atiq ur-Rehman, director of a hospital in Peshawar, said of the CIA ruse.

One health official in the border belt said the main concern is that militants in that region might harm members of vaccination teams, suspecting them of being CIA agents. Another health official in Peshawar said that this week’s drive was nearly canceled out of concern about fallout from the CIA plot.

Pakistan is one of four nations — along with India, Afghanistan and Nigeria — where polio is endemic, and it is the only one where cases are rising. In the first six months of this year, 59 cases were reported.

President Asif Ali Zardari declared polio a national emergency in January, and donors from across the globe are funding a $137.5 million emergency plan to stop transmission in Pakistan by 2012. The plan noted, with a hint of shame, that Pakistan risked pariah status if rising polio statistics “isolate the country in a world that wants to protect its citizens” from the virus.

According to U.S. and Pakistani officials, a doctor named Shakil Afridi, who previously worked on anti-polio programs in the tribal areas, was paid to carry out a hepatitis B vaccine program in the city where bin Laden lived, Abbottabad. Afridi is now in the custody of Pakistan’s intelligence agencies, and U.S. officials are lobbying for his release.

A senior U.S. official defended the campaign last week, saying it involved actual hepatitis vaccine and was not a “fake public-health effort.” Had the effort succeeded in collecting bin Laden family DNA, it could have helped U.S. officials confirm the al-Qaeda leader’s presence in Abbottabad before the raid.

“The vaccination campaign was part of the hunt for the world’s top terrorist, and nothing else,” the official said. “If the United States hadn’t shown this kind of creativity, people would be scratching their heads asking why it hadn’t used all tools at its disposal to find bin Laden.”

While privately expressing anger at the CIA program, most Pakistani officials and health organizations here have chosen to keep quiet about it in public. The hope is that less damage will be done if word does not circulate widely, they said. Health officials said this week that the anti-polio drive, one of several each year, seemed unaffected, though they cautioned that injected immunizations might elicit more suspicion. The polio vaccine is oral.

The government has recruited Muslim leaders to counter the anti-vaccine diatribes of radical clerics. Maulana Jalil Jan, a Peshawar cleric who is a member of a polio awareness committee, said he and others came on board after reassurances that immunization programs also receive funding from Arab nations and that there is no medical evidence that they cause sterilization.

“We are using our mosques and our influence, not only in the urban centers but in the remotest parts,” Jan said.

Nima Abid, the World Health Organization’s polio team leader in Pakistan, said that about 2 percent of people approached nationwide during anti-polio campaigns refuse the vaccine. That is not an insignificant number: This week, the campaign sought to immunize 52 million children younger than 5. Polio is highly contagious, and for each child paralyzed, Abid said, 199 are infected.

Refusals, as they are known, primarily occur in the northwest, where Islamist militants hold sway and health teams depend on help from the Pakistani military. In some parts of the rugged tribal areas, combat or insurgents prevent vaccine teams’ entrance, Abid said.

In Peshawar, a bustling city dotted with crowded “high-risk” polio areas, there have been three cases this year, said Janbaz Afridi, who directs the immunization programs for the city and its surrounding province, Khyber Pakhtunkhwa. This week, more than 10,000 temporary hires pitched vaccines on roadways connecting to the tribal areas, in nearby refugee camps and on house-to-house tours.

Outside a bus depot, Zeeshan Khan, 18, stood with a blue cooler full of vaccines, a clipboard and a purple pen to mark the fingernails of vaccinated children. He had given 17 vaccinations since that morning, he said, and all parents approached had agreed.

Mujahid Shah, 22, who had just arrived with his 3-year-old son from the border region, was one. He said: “It is for the good of the child.”

Special correspondent Haq Nawaz Khan contributed to this report.