A top White House official has promised that the Central Intelligence Agency will never again use vaccination programs as a cover for spying, three years after the agency set up a fake immunisation program in Pakistan in its hunt for Osama bin Laden.

Lisa Monaco, a senior counterterrorism and homeland security adviser to President Obama, wrote in a letter addressed to the leaders of several prominent public health schools that the CIA would not use immunisation programs – or workers – as a means to collect intelligence. Such programs have prompted attacks on medical workers in Pakistan.

"The Director of the Central Intelligence Agency directed in August 2013 that the agency make no operational use of vaccination programs, which includes vaccination workers," Monaco wrote in the letter, which was first obtained by Yahoo News.

"Similarly, the agency will not seek to obtain or exploit DNA or other genetic material acquired through such programs. This CIA policy applies worldwide and to US and non-US persons alike."

The letter was written in response to a January 2013 letter signed by the deans of 12 public health schools that sharply criticised the CIA's use of a vaccination campaign ruse to target Bin Laden.

In the months leading up to the May 2011 raid that killed the al-Qaida leader, the CIA enlisted the help of Pakistani doctor Shakil Afridi, who would give hepatitis B vaccinations in an attempt to pinpoint Bin Laden's whereabouts. The failed plot aimed to obtain DNA samples from Bin Laden's children that could be compared with samples from his late sister, which would prove the family was living in the compound. Afridi was arrested by Pakistan's Inter-Services Intelligence agency (ISI) for working with American intelligence agents and remains in jail in Pakistan.

Since the ploy was made public, anti-polio campaigns have become targets for deadly attacks by militants in Pakistan, where the vaccine was already controversial. The BBC reports that more than 60 polio workers and security personnel were killed between December 2012 and April 2014.

In 2012, two militant commanders banned anti-polio health teams from carrying out their work in retaliation for the CIA's lethal drone strikes. The threats were effective, and in the region some parents refused to have their children vaccinated against the disease. Parents who defy the Taliban and vaccinate their children against polio must do so in secret.

Earlier this month, the World Health Organisation (WHO) warned that polio has re-emerged as a public health emergency in Pakistan. The virus currently affects 10 countries worldwide, with Pakistan among only three countries in the world where polio remains endemic.

Since the beginning of the year, 77 cases of polio have been reported – 61 of them in Pakistan, according to the Global Polio Eradication Initiative, an organisation spearheaded by the WHO that aims to end the spread of polio. In 2013, a total of 416 cases of polio were reported, 93 of them in Pakistan.

Polio is a crippling disease that can be fatal. Although there is no cure, the polio vaccine has helped eradicate the virus in most parts of the world.

The WHO has called for international travel restrictions on people coming from Pakistan, as well as Cameroon and Syria, and recommends that residents and long-term visitors of these countries receive polio vaccines before international travel.