The low-ranking health department employees were punished for helping Dr Shakil Afridi, who was assigned by the CIA to set up a fake vaccination scheme in Abbottabad, ahead of the 3 May US military operation that found and killed the al-Qaida leader there.

In July last year, the Guardian revealed that Afridi was hired by the American spy agency, which was trying to establish whether Bin Laden was living inside a compound to which it had tracked an al-Qaida “courier”.

Afridi used unwitting local health visitors to go house to house to vaccinate Abbottabad residents for hepatitis B, with the aim of getting inside the suspected Bin Laden home and extracting DNA from one of his children. The al-Qaida leader had habitually lived with many members of his large family even while on the run. The scheme, apparently unsuccessful, was run in the weeks before the 3 May raid.

The fate of Afridi, who was arrested by the Pakistan military’s Inter-Services Intelligence (ISI) agency in late May last year, and remains in their custody, has added to a break-down in relations between Washington and Islamabad. American officials are pressing Pakistan to free Afridi, to allow him to travel to the US, where he would be resettled. However, he faces possible treason charges at home for working for a foreign intelligence agency.

The sacked health workers would have known nothing of the true purpose of the vaccination programme. They include all the 15 of the women health workers employed in Nawa Sher, the district of Abbottabad where Bin Laden had lived, plus two more senior health officials in the town. Among the fired employees is a nurse known as Bakhto, whose full name is Mukhtar Bibi. She is believed to have got inside the bin Laden compound with the vaccination programme.

Afridi was a senior health official posted in a part of the tribal area, far from Abbottabad, which was way outside his jurisdiction. He travelled to Abbottabad and used the health workers there without the knowledge of the senior Abbottabad administration.

Zafeer Ahmed, in charge of health services for Abbottabad, said that the 17 were dismissed for breaking the rules.

“There was negligence as these workers did not have permission from the provincial government or the health department to work with Shakil Afridi,” said Ahmed. “I was ordered by the provincial government to take action against them.”

A provincial government inquiry into the affair is on-going and higher ranking health officials could be disciplined in future.

No Pakistani official has been held responsible for failing to detect Bin Laden’s presence in the country.

The sacked women health workers would be paid little but would probably have been dependent on government employment to make ends meet for their families.

The CIA scheme, as well as having grave consequences for Afridi, and now triggering the dismissal of health officials, has damaged vaccination programmes throughout Pakistan, including for polio, as it greatly added to wild rumours that the medicines are actually an American conspiracy to sterilise Pakistanis.

Afridi was earlier this month reportedly removed from his post, while his wife was separately dismissed from her government job, running a girls’ college in the north west.

In January this year, the former CIA chief, Leon Panetta, now the US Defence Secretary, publicly called for Afridi’s release, acknowledging his role for the first time in the hunt for Bin Laden. American officials believe that Afridi should be lauded for his services, not punished.

“I am very concerned about what the Pakistanis did with this individual [Afridi]. This was an individual who, in fact, helped provide intelligence that was very helpful with regard to this operation,” Panetta had said.

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As part of extensive preparations for the raid that killed Bin Laden in May, CIA agents recruited a senior Pakistani doctor to organise the vaccine drive in Abbottabad, even starting the “project” in a poorer part of town to make it look more authentic, according to Pakistani and US officials and local residents.

The doctor, Shakil Afridi, has since been arrested by the Inter-Services Intelligence agency (ISI) for co-operating with American intelligence agents.

Relations between Washington and Islamabad, already severely strained by the Bin Laden operation, have deteriorated considerably since then. The doctor’s arrest has exacerbated these tensions. The US is understood to be concerned for the doctor’s safety, and is thought to have intervened on his behalf.

The vaccination plan was conceived after American intelligence officers tracked an al-Qaida courier, known as Abu Ahmad al-Kuwaiti, to what turned out to be Bin Laden’s Abbottabad compound last summer. The agency monitored the compound by satellite and surveillance from a local CIA safe house in Abbottabad, but wanted confirmation that Bin Laden was there before mounting a risky operation inside another country.

DNA from any of the Bin Laden children in the compound could be compared with a sample from his sister, who died in Boston in 2010, to provide evidence that the family was present.

So agents approached Afridi, the health official in charge of Khyber, part of the tribal area that runs along the Afghan border.

The doctor went to Abbottabad in March, saying he had procured funds to give free vaccinations for hepatitis B. Bypassing the management of the Abbottabad health services, he paid generous sums to low-ranking local government health workers, who took part in the operation without knowing about the connection to Bin Laden. Health visitors in the area were among the few people who had gained access to the Bin Laden compound in the past, administering polio drops to some of the children.

Afridi had posters for the vaccination programme put up around Abbottabad, featuring a vaccine made by Amson, a medicine manufacturer based on the outskirts of Islamabad.

In March health workers administered the vaccine in a poor neighbourhood on the edge of Abbottabad called Nawa Sher. The hepatitis B vaccine is usually given in three doses, the second a month after the first. But in April, instead of administering the second dose in Nawa Sher, the doctor returned to Abbottabad and moved the nurses on to Bilal Town, the suburb where Bin Laden lived.

It is not known exactly how the doctor hoped to get DNA from the vaccinations, although nurses could have been trained to withdraw some blood in the needle after administrating the drug.

“The whole thing was totally irregular,” said one Pakistani official. “Bilal Town is a well-to-do area. Why would you choose that place to give free vaccines? And what is the official surgeon of Khyber doing working in Abbottabad?”

A nurse known as Bakhto, whose full name is Mukhtar Bibi, managed to gain entry to the Bin Laden compound to administer the vaccines. According to several sources, the doctor, who waited outside, told her to take in a handbag that was fitted with an electronic device. It is not clear what the device was, or whether she left it behind. It is also not known whether the CIA managed to obtain any Bin Laden DNA, although one source suggested the operation did not succeed.

Mukhtar Bibi, who was unaware of the real purpose of the vaccination campaign, would not comment on the programme.

Pakistani intelligence became aware of the doctor’s activities during the investigation into the US raid in which Bin Laden was killed on the top floor of the Abbottabad house. Islamabad refused to comment officially on Afridi’s arrest, but one senior official said: “Wouldn’t any country detain people for working for a foreign spy service?”

The doctor is one of several people suspected of helping the CIA to have been arrested by the ISI, but he is thought to be the only one still in custody.

Pakistan is furious over being kept in the dark about the raid, and the US is angry that the Pakistani investigation appears more focused on finding out how the CIA was able to track down the al-Qaida leader than on how Bin Laden was able to live in Abbottabad for five years.

Over the weekend, relations were pummelled further when the US announced that it would cut $800m (£500m) worth of military aid as punishment for Pakistan’s perceived lack of co-operation in the anti-terror fight. William Daley, the White House chief of staff, went on US television on Sunday to say: “Obviously, there’s still a lot of pain that the political system in Pakistan is feeling by virtue of the raid that we did to get Osama bin Laden, something the president felt strongly about and we have no regrets over.”

The CIA refused to comment on the vaccination plot.

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