WASHINGTON - As Pakistan faces the resurgence of polio, the CIA said it will no longer use vaccination programmes to cover spying operations, the agency and a White House official confirmed.

The new policy, which was instituted by CIA Director John Brennan in August 2013, had not previously been made public. President Barack Obama’s top counterterrorism and homeland security adviser, Lisa Monaco, sent out a letter to the deans of 13 public health schools last week, which stated the policy had been put in place.

“The CIA will make no operational use of vaccination programmes which include vaccination workers. Similarly, the agency will not seek to obtain or exploit DNA or other genetic material acquired through such programmes,” Monaco wrote in the letter. “This CIA policy applies to US and non-US persons alike.”

The Central Intelligence Agency had enlisted Pakistani doctor Shakil Afridi to collect intelligence under the guise of an immunisation effort in Abbottabad as part of planning for the May 2011 raid on Osama bin Laden’s compound there.

The agency aimed to confirm intelligence that bin Laden was at the compound by comparing DNA obtained from children living there to a sample from the fugitive al-Qaeda chief’s late sister.

Even before those revelations, the Taliban in Pakistan had already opposed Western-backed vaccination campaigns, claiming that they were secret efforts to sterilise Muslim children. But the CIA’s actions helped fuel an armed backlash against immunisation workers, reportedly killing 56 people between December 2012 and May 2014. The victims include not just medical workers but police officers assigned to guard them.

Another result of the CIA’s actions was to lead many Pakistani parents to forgo vaccinations for ailments like polio. The crippling and sometimes fatal illness has no known cure, but there are several safe and effective vaccines, according to the Centers for Disease Control.

Of the 77 documented new cases of polio worldwide in calendar year 2014, 61 were in Pakistan, mostly from the remote and restive Federally Administered Tribal Areas (FATA) region, which serves as a Taliban stronghold.

Earlier this month, the World Health Organisation imposed travel restrictions on anyone coming from Pakistan, one of just three countries in the world where polio is still endemic. The rules, to be implemented on June 1, will require travellers, leaving the country to have polio vaccination certificates.

Ms Monaco’s letter came nearly one and a half years after the deans of 12 schools of public health wrote a letter to Obama, saying that “as a general principle, public health programmes should not be used as cover for covert operations.”

“While political and security agendas may by necessity induce collateral damage, we as an open society set boundaries on these damages and we believe this sham vaccination campaign exceeded those boundaries,” they wrote, referring to the CIA’s hoax campaign.

CIA Director Brennan made the decision himself because he “took seriously the concerns raised by the public health community,” CIA spokesman Todd Ebitz said.

“By publicising this policy, our objective is to dispel one canard that militant groups have used as justification for cowardly attacks against vaccination providers,” Ebitz said by email.