Before launching the high-risk operation against bin Laden, US officials wanted to test DNA samples from people living at the compound with a sample that they had from his sister. Doctor Afridi, backed by US intelligence, first launched the programme in Abbottabad's poorest area to make it appear more credible.
The project then moved swiftly to the Bilal Town suburb, where bin Laden was residing.
"The whole thing was totally irregular," a Pakistani official reportedly said. "Bilal Town is a well-to-do area. Why would you choose that place to give free vaccines?"
A nurse managed to gain access to the compound but Pakistani sources claim she failed to obtain any DNA samples.
The Pakistani government has so far set up a panel to probe the raid in the northwestern city of Abbottabad, as well as how bin Laden managed to hide there. The commission has visited bin Laden's compound, and questioned civil and military officials.
Bin Laden's widows and the accused doctor have been in Pakistani custody since shortly after the raid and US officials have been seeking the doctor's release since his arrest.
Panetta remains convinced that someone in the Pakistani government "must have had some sense" that a person of interest was in the compound. He added that he has no proof that Pakistan knew it was bin Laden.
The Pakistani government had hoped to resolve the Afridi matter quietly, once media attention died down, perhaps releasing him to US custody, according to two Pakistani officials. They requested anonymity because the investigation into charges the doctor behaved treasonously was continuing.
Washington has declared that it would suspend $800 million (£509 million) worth of security aid amid growing frustration over Islamabad's refusal to pursue Afghan Taliban militants who launch attacks on U.S. and North Atlantic Treaty Organisation forces in Afghanistan from strongholds in Pakistan.
The Pakistani military hit back this week, insisting it was capable of fighting Islamic militants without US assistance. Pakistani officials are adamant that the US special forces raid on the terrorist’s hideout was a violation of Pakistan’s national souvereignty and solidarity.
Bin Laden was killed on May 2 in a raid that inflamed increasingly souring US-Pakistan relations.