Declan Walsh reports: In the shadows of the American operation that killed Osama bin Laden, the fate of a small-town Pakistani doctor recruited by the C.I.A. to help track the Qaeda leader still looms between the two countries, a sore spot neither can leave untouched.

Picked up by Pakistani intelligence agents days after the Bin Laden raid a year ago and now in secret detention, the doctor, Shakil Afridi, has embodied the tensions between Washington and Islamabad. To some American officials he is a hero, worthy of praise and protection; Defense Secretary Leon E. Panetta has personally appealed for his release. But inside Pakistan’s powerful military, still smarting from the raid on its soil, he is seen as a traitor who should face treason charges that could bring his execution. “We need to make an example of him,” one senior intelligence official said.

Beyond hard feelings and talk, however, his case has had a much wider effect: It has also roiled the humanitarian community in Pakistan, giving rise to a wave of restrictions that have compromised multimillion dollar aid operations serving millions of vulnerable Pakistanis.

Hardest hit is Save the Children, the largest international aid agency in Pakistan.

Dr. Afridi has told interrogators for the top Pakistani military intelligence agency, the ISI, that he was introduced to the C.I.A. through Save the Children, according to Pakistani officials and Western aid workers. Save the Children vigorously denies the claim, saying it has been made a scapegoat by a desperate man who, according to senior American officials, has been tortured in Pakistani custody. Nevertheless his claims have had a stark impact on an organization that says it spent $105 million last year helping seven million Pakistanis, most of them women and children.

Senior managers have been forbidden from leaving the country, other staff members have been refused visas, and aid supplies have been blocked by customs officials, depriving an estimated 35,000 infants of medical care over a three-month period. Pakistani intelligence has monitored the phone calls and residences of Save the Children staff.

Other aid groups complain of problems, too, largely at the hands of Pakistani officials convinced that their employees could be spies. To them, the affair sheds new light on a murky practice that they say should never take place: the recruitment of aid workers as intelligence operatives in a sensitive country like Pakistan, already awash in conspiracy theories about Western meddling. [Continue reading…]