The newly disclosed CIA policy mandates that it will not use vaccination programmes as part of its spy operations, according to senior Obama administration officials.
The directive by CIA Director John Brennan, made nine months ago but made public now, followed concerns raised by leaders of a dozen US public health schools in a letter to President Barack Obama.
They spoke out following revelations the CIA had enlisted Shakil Afridi, a Pakistani doctor, to oversee a false immunisation campaign in the country ahead of the 2011 raid that killed al Qaeda chief bin Laden in the garrison city of Abbottabad.
The public health programmes reached out to Obama after the organisation Save the Children was forced to "withdraw all foreign national staff" from Pakistan as a "result of a CIA sham vaccination campaign."
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Save the Children was in the midst of a campaign to administer the polio vaccination in Pakistan, one of the few places left in the world where the virus is still prevalent.
In their letter to the White House in January 2013, the deans also alleged that "seven or more United Nations health workers who were vaccinating Pakistani children against polio were gunned down in unforgivable acts of terrorism" as a result of the CIA effort.
"Similarly, the agency will not seek to obtain or exploit DNA or other genetic material acquired through such programmes," the letter to the deans said.
CIA spokesman Dean Boyd told CNN that Brennan established the policy "after carefully considering a variety of views, including those from outside the agency.
Boyd also said it "is important to note that militant groups have a long history of attacking humanitarian aid workers in Pakistan and those attacks began years before the raid against the bin Laden compound."
Islamists allege that that US spies get mixed with the polio workers to get information about insurgents. They also allege that anti polio oral drops is a western conspiracy to reduce fertility among Muslims to check demographic changes.