If PM Modi had flown over Pakistan it would have taken three-and-a-half hours to reach Bishkek and now it will take about seven hours for the journey, officials said.
The decision also came over a week after Pakistan Prime Minister Imran Khan and foreign minister Shah Mehmood Qureshi wrote separate letters to their Indian counterparts, pushing for restarting bilateral talks.
India has not been engaging with Pakistan since an attack on the Air Force base at Pathankot in January of 2016 by a Pakistan-based terror group, maintaining that talks and terror cannot go together.
Pakistan PM Imran Khan will also be attending the summit, however, PM Modi and Pak PM Imran Khan are not slated to meet at Bishkek.
Last month, Pakistan had given special permission to the then external affairs minister Sushma Swaraj to fly through Pakistani airspace while travelling to Bishkek to attend a meeting of SCO Foreign Ministers.
Pakistan fully closed its airspace on February 26 after the Indian Air Force struck a Jaish-e-Mohammed (JeM) terrorist training camp in Balakot.
Since then, it has only opened two routes, both of them pass through southern Pakistan, of the total 11.
On its part, the IAF announced on May 31 that all temporary restrictions imposed on Indian airspace post the Balakot airstrike have been removed.
If PM Modi had flown over Pakistan it would have taken three-and-a-half hours to reach Bishkek and now it will take about seven hours for the journey.