Shakil Afridi was accused of running a CIA-sponsored fake vaccine programme in Abbottabad, where bin Laden was killed last year on May 2 in a covert US operation. His programme was aimed at obtaining DNA samples from any of bin Laden's family members residing in the compound.
A Pakistani commission investigating the US raid that killed bin Laden had called for Afridi's trial on charges of high treason.
Official sources said that Afridi was awarded jail term under the tribal laws, known as Frontier Crimes Regulations (FCR). The British-era FCR is still effective in Pakistan's tribal regions.
Afridi was sent to main prison in the northwestern city of Peshawar, sources said.
The government has already sacked him from services and other nursing staff who worked on his instruction.
US Defence Secretary Leon Panetta admitted in January that Afridi had helped American intelligence by collecting DNA to verify al-Qaeda chief's presence.
Washington has been arguing that Afridi should be freed and allowed to live in the US.
A group of US lawmakers had requested the Obama administration to honour Afridi for helping the US.
There had been no official confirmation if any DNA from bin Laden or any of his family members was ever obtained from his hideout. (MORE)