Vajpayee will receive Sourav Ganguly's men at his residence on Wednesday, a few hours before the team departs for Lahore by a special Indian Airlines flight.
"Considering the importance of the goodwill tour, the Prime Minister will personally meet the team members and extend his good wishes to them," a Board of Control for Cricket in India (BCCI) release said on Thursday.
It was on Vajpayee's insistence that the Government lifted a three-year ban on bilateral sporting ties with Pakistan in October following a thaw in diplomatic relations between the warring neighbours.
Vajpayee, who initiated peace moves with Pakistan last April, intervened a second time last month when the tour was put in doubt following reports that security agencies wanted it postponed till after the Indian general elections in April-May.
Sporting teams in India are not normally granted an audience with the Head of Government before an event, but official receptions are held on their return if they have turned in an exceptional performance.
The Indian team, which will undergo a three-day conditioning camp in Kolkata from Sunday, will arrive in New Delhi a day before their departure.
Besides meeting with the Prime Minister, the team will also attend briefings by security agencies and the foreign office, the BCCI release said.
Media reports on Thursday quoted Government officials as saying that a four-member security detail will accompany the team on the 40-day tour.
It includes Yashovardhan Azad, an intelligence official in the VIP division of the home ministry, who toured Pakistan with a BCCI delegation last month to oversee arrangements at various venues.
The other members of the security team are three senior police officials Manoj Lal, Dharmendra Kumar and Prabhakar, who like many Indians uses only one name.
India last played a Test series in Pakistan in 1989, but crossed the borders for a week-long tour in 1997 for three One-day Internationals.