Médecins Sans Frontières has lashed out at the CIA for using a fake vaccination programme as a cover to spy on Osama bin Ladenon Thursday, saying it threatened life-saving immunisation work around the world.

The international medical aid charity said the ploy used by US intelligence, revealed this week in the Guardian, was a "grave manipulation of the medical act".

The CIA recruited a Pakistani doctor and health visitors before the operation in May that killed Bin Laden in Abbottabad in northern Pakistan, to try to ascertain whether the al-Qaida leader was living in the compound. The doctor, Shakil Afridi, set up a vaccination drive for Hepatitis B in the town in order to try to gain entry to the Bin Laden compound and obtain DNA samples from those living there.

On Thursday night, a senior US government official defended the practice, saying it had been intended as "an actual vaccination campaign conducted by real medical professionals". He said the team was supposed to deliver the full course of three vaccinations to those treated in Abbottabad.

The official, who spoke on condition of anonymity, added: "And it's not as if this kind of campaign is something the CIA runs every day."

However, on the ground in Abbottabad the Guardian discovered that while the vaccine doses themselves were genuine, the medical professionals involved were not following procedures. In an area called Nawa Sher, they did not return a month after the first dose to provide the required second batch. Instead, according to local officials and residents, the team moved on, in April this year, to Bilal Town, the suburb where Bin Laden lived.

"The risk is that vulnerable communities – anywhere – needing access to essential health services will understandably question the true motivation of medical workers and humanitarian aid," said Unni Karunakara, MSF's international president. "The potential consequence is that even basic healthcare, including vaccination, does not reach those who need it most."

Afridi was arrested in late May by Pakistani intelligence, for working for a foreign spy agency. The United States is pressing Pakistan to let him go and allow the doctor and his family to be resettled in the US. Islamabad is infuriated by the CIA's activities inside the country, which were kept secret from their Pakistani counterparts.

"It is challenging enough for health agencies and humanitarian aid workers to gain access to, and the trust of, communities, especially populations already sceptical of the motives of any outside assistance," said MSF. "Deceptive use of medical care also endangers those who provide legitimate and essential health services."

The impact of the fake vaccination drive may be keenly felt in Pakistan, where the public already sees an American conspiracy everywhere. Polio campaigns could be at particular risk, as Pakistan has the biggest polio problem in the world.

The US official said: "The vaccination campaign was part of the hunt for the world's top terrorist, and nothing else. If the United States hadn't shown this kind of creativity, people would be scratching their heads asking why it hadn't used all tools at its disposal to find Bin Laden."

The CIA has not publicly admitted that it used the doctor. A CIA spokesman, George Little, would only say: "Finding Osama Bin Laden is a major victory for the United States and Pakistan."