The decision by the Union Home Ministry came after Islamabad raised concerns over the safety of its athletes following the disruption of a concert by Pakistani ghazal singer Ghulam Ali and attack on politician Sudheendra Kulkarni for organising the launch of a book by Pakistan Foreign Minister Khurshid Mahmud Kasuri in Mumbai.
The Games, which is being hosted by Assam and Meghalaya, begins tomorrow.
Since Guwahati and Kolkata airports are close to the venues of the Games, they have been added to the designated entry points for Pakistani passport holders and non-validated pass (NVP) holders during the period of South Asian Games, a Home Ministry official said.
India, on a reciprocal basis, too, allows entry through four designated check-point: Attari-Wagah, Delhi, Mumbai and Chennai.
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This is perhaps the first time that two new entry points have been designated for Pakistanis, albeit only for sportspersons and officials for the duration of the South Asian Games.
Sri Lanka, Bangladesh, Myanmar, Nepal, Bhutan and Afghanistan are also taking part in this sporting event.
The Home Ministry will treat NVPs issued to all foreign athletes and officials after proper accreditation and security clearance as multiple-entry visa.
Foreign officials and athletes other than Pakistanis can enter India at seven entry points: Kolkata, Delhi, Mumbai, Chennai, Bengaluru, Guwahati and Dowki (Meghalaya).
Prime Minister Narendra Modi will grace the inauguration ceremony.