An alliance of 200 US aid groups has written to the head of the CIA to protest against its use of a doctor to help track Osama bin Laden, linking the agency's ploy to the polio crisis in Pakistan.

The country recorded the highest number of polio cases in the world last year, a health catastrophe that threatens to spiral out of control.

In July the Guardian revealed that the CIA used a Pakistani doctor, Shakil Afridi, in the hunt for Bin Laden. In the weeks before the 3 May operation to kill Bin Laden, Afridi was instructed to set up a fake vaccination scheme in the town of Abbottabad, in order to gain entry to the house where it was suspected that the al-Qaida chief was living, and extract DNA samples from his family members.

However the ruse has provided seeming proof for a widely held belief in Pakistan, fuelled by religious extremists, that polio drops are a western conspiracy to sterilise the population.

"The CIA's use of the cover of humanitarian activity for this purpose casts doubt on the intentions and integrity of all humanitarian actors in Pakistan, thereby undermining the international humanitarian community's efforts to eradicate polio, provide critical health services, and extend life-saving assistance during times of crisis like the floods seen in Pakistan over the last two years," the InterAction coalition wrote to the CIA director, David Petraeus.

The group, which includes the International Rescue Committee, Mercy Corps and Care, said that as well as damaging the drive against polio and other health problems in Pakistan, the CIA's tactics had endangered the lives of foreign aid workers. In recent months, at least five international NGO workers, including a British doctor, have been kidnapped by presumed Islamic extremists.

"The CIA-led immunisation campaign compromises the perception of US NGOs as independent actors focused on a common good, and casts suspicion on their humanitarian workers. The CIA's actions may also jeopardise the lives of humanitarian aid workers in Pakistan," the letter said.

The letter was prompted by the fact that in January this year, a senior US official, the defence secretary, Leon Panetta, publicly acknowledged the role that Afridi had played.

The CIA was unsure whether the al-Qaida chief was really living in Abbottabad. Afridi used nurses to go house to house to offer vaccinations for hepatitis, managing to gain entry to the house where Bin Laden was suspected of living. The idea may have come from the fact that a nurse had in the past managed to get into the Bin Laden compound to administer polio drops to the many children living there - his children and grandchildren, it turned out.

Washington has been pressuring Pakistan to release Afridi, who was arrested by the Pakistani authorities some three weeks after the Bin Laden raid. This week, the US secretary of state, Hillary Clinton, said that Pakistan had no basis for holding Afridi.