For six assembly constituencies of Gurdaspur district, counting centre has been set up at Sukhjindra College Gurdaspur and for three assembly constituencies of Pathankot district, counting centre has been set up at the SD College in Pathankot.
Tight security arrangements have been made at the counting centres, an official said. The counting started at 8 am.
Gurdaspur Lok Sabha bypoll witnessed a three-cornered race contest among major political parties -- the Congress, the BJP and the AAP.
The bypoll is seen as a barometer for the popularity of the six-month-old Congress government in Punjab.
Congress candidate Sunil Jakhar had earlier claimed the bypoll would be a "referendum" on the Modi government. The BJP had also tried pulling out all the stops to retain the seat, which Khanna had won four times on its ticket.
A victory would give a much-needed boost to the BJP, which had bagged just one segment of Sujanpur out of the four seats it had contested in the assembly polls.
The AAP, the main opposition party in Punjab with 20 seats in the House, was also looking to strengthen its presence in the state with a victory in the bypoll.
The result will decide the fate of total 11 candidates including Congress nominee Sunil Jakhar, BJP's Swaran Salaria and AAP's Major General (retd) Suresh Khajuria.
Out of nine assembly segments falling in Gurdaspur Lok Sabha seat, Dera Baba Nanak Vidhan Sabha constituency had registered maximum voting percentage at 65 per cent while the Batala Vidhan Sabha constituency had witnessed lowest voting percentage at 50 per cent, an official said.
The polling percentage in the nine assembly segments was also lower than what was recorded in 2017 assembly elections.
Gurdaspur Lok Sabha seat has been a stronghold of the BJP. Actor-turned-politician Vinod Khanna had remained four-time MP from Gurdaspur Lok Sabha seat. Khanna had died of cancer at a hospital in Mumbai on 27 April this year.