The United States ran a fake vaccination program in the Pakistani town of Abbottabad ahead of the raid that killed Osama bin Laden, in a bid to gather DNA confirmation of his presence there.

The Guardian newspaper reported that as part of the elaborate ruse a Pakistani doctor recruited by the Central Intelligence Agency gained access to the Al Qaeda leader's walled compound but failed to meet Bin Laden.

U.S. officials have said that despite months of monitoring by satellites and agents in a secret safe house nearby, they had not confirmed Bin Laden's presence in the Abbottabad compound when they launched the special forces raid in May that led to his killing.

The vaccination plan, carried out with the assistance of local doctor Shakil Afridi, was intended to gain DNA from the Saudi's children, which could have been compared with a sample from his sister who died in Boston in 2010 to confirm the Bin Laden family was present in Abbottabad.

The doctor, who has been arrested by Pakistani authorities and remains in custody, paid "generous sums" to local health workers to participate in the free Hepatitis B immunization program.

He put up posters for the vaccination drive, recruited several nurses and started it in a poor neighborhood before moving on to the more wealthy area where Bin Laden was suspected to be hiding, The Guardian said.

A nurse did enter the compound but sources told The Guardian and The New York Times that the ruse failed to gain any DNA from Bin Laden's relatives.

Pakistan has not formally commented on Afridi's arrest, but one official told The Guardian: "Wouldn't any country detain people for working for a foreign spy service?"

The revelations are likely to further strain relations between Islamabad and Washington, which have been near breaking point since the Bin Laden raid embarrassed the Pakistani military and raised questions over how much it knew about the Al Qaeda chief's whereabouts.

In the latest blow to the alliance, the United States announced on the weekend it was cutting $800 million in military aid to Pakistan over Islamabad's alleged lack of co-operation in the struggle against terror.