Shakil Afridi faces 33 years in jail in Pakistan despite calls from senior US officials to release him

The Pakistani medical official who ran a fake CIA vaccination programme to help find Osama bin Laden has been jailed for 33 years.

A spokesman for Khyber Agency, an administrative unit in Pakistan's restless frontier, said Dr Shakil Afridi would face decades in jail – despite calls from senior US officials to release the man who helped with efforts to track down the al-Qaida chief.

The tough sentence for the former surgeon general of Khyber will be taken as another sign of the terrible state of US-Pakistan relations.

And it will further alarm western critics of Pakistan who say the country has put far more effort into trying to understand how US spies and special forces were able to plan and launch the Bin Laden raid than into how the al-Qaida leader was able to remain for so long in the Pakistani army garrison town of Abbottabad.

The sentence was announced just days after Barack Obama snubbed the Pakistani president, Asif Ali Zardari, by refusing to hold a formal meeting with him at the Nato conference in Chicago.

In January Leon Panetta, the US defence secretary, said he was "very concerned" about the arrest of Afridi after Pakistan's intelligence service discovered he had set up a fake hepatitis B vaccination scheme with his nurses going from house to house in Abbottabad in the weeks before the raid on Bin Laden's hideout in May last year.

"For them to take this kind of action against somebody who was helping to go after terrorism, I just think it is a real mistake on their part," Panetta said in January.

There had been hopes that Afridi would eventually be quietly released after the controversy surrounding the Bin Laden raid had subsided.

US intelligence officials say the clandestine operation by Afridi did not succeed in determining whether Bin Laden was in the house and the raid went ahead without any certainty that the Navy Seal team would find its target.

However, Pakistani security officials recently told the Guardian that although the nurses working for Afridi were not allowed inside the house to vaccinate any of the children, they did succeed in getting a mobile phone number for someone in the house.

The Pakistani sources say that phone call allowed the CIA to make a voice match to Bin Laden's private courier, a man known as Abu Ahmed al-Kuwaiti.

US aid groups have complained that the bogus vaccination operation undermined their efforts "to eradicate polio, provide critical health services, and extend life-saving assistance during times of crisis" in Pakistan. The ruse may have fuelled fears, backed by religious extremists, that polio drops are a western conspiracy to sterilise the population.