External Affairs Ministry spokesman Raveesh Kumar said the VVIP aircraft will fly via Oman, Iran and the Central Asian countries on way to Bishkek.
"Government of India had explored two options for the route to be taken by the VVIP aircraft to Bishkek for the SCO Summit. A decision has now been taken that the VVIP aircraft will fly via Oman, Iran and Central Asian countries on the way to Bishkek," he said.
The decision is a clear snub to Pakistan, which on Monday had reportedly said that it had decided "in principle" to allow the Indian Prime Minister's plane to fly over its airspace for the flight to Bishkek.
After India carried out air strike at Jaish-e-Mohammad (JeM) terror camp in Balakot on February 26, Pakistan had completely shut down its airspace but lately it has opened two routes which pass through southern parts of the country.
The air strike was conducted in retaliation to the ghastly attack carried out by the JeM on a CRPF convoy in Kashmir's Pulwama, in which 40 personnel were killed.
Ever since, the relations between India and Pakistan have witnessed a new low and saw even heightened military tensions in between.
The Prime Minister is travelling to Bishkek on Thursday morning to attend the annual SCO Summit and flying via Pakistan would have provided a shorter route.
Pakistan Prime Minister Imran Khan will also attend the Summit but according to Raveesh Kumar, no bilateral meeting between them has been arranged.
Modi will have bilateral talks with other leaders of the eight-nation SCO grouping, including Russian President Vladimir Putin and Chinese President Xi Jinping.
At the Summit, Modi is expected to highlight the dangers posed to the world by state-sponsored terrorism, a clear reference to Pakistan.
( With inputs from IANS )