External Affairs Ministry spokesman Raveesh Kumar said that the Prime Minister's VVIP aircraft will fly via Oman, Iran and the Central Asian countries on way to Bishkek.
Sources also revealed that before Abhinandan was moved to Rawalpindi by Pakistan's ISI operatives, he was treated well by the Pakistan Army.
Modi said that his visit was intended to send a message that India does "not bear any ill-will towards Pakistan".
Pakistan's Foreign Minister Shah Mehmood Qureshi, during the peak of India-Pakistan tensions following the Pulwama terror attack had admitted that Azhar was in Pakistan.
In a big diplomatic win for India, Masood Azhar was designated a global terrorist by the UNSC on Wednesday.
The sources said the listing was based on evidence, which was not supposed to be a biodata of a terrorist that all terror acts committed by him would be listed.
Pakistan foreign office spokesman Mohammad Faisal rejected the world body's move as a 'victory for India and validation of its stance' as projected by the Indian media.
'Baseless charge': Pakistan after India stops cross LoC trade to curb illegal arms, drugs, fake notes
The NIA claims that Pakistani trading concerns are being operated by persons linked to outfits involved in fuelling terrorism.
IAF remarks came after a report in US-based Foreign Policy magazine said the US personnel recently counted Pakistan's F-16s and found none of the planes missing.
Sources said Pakistan was not going ahead with a previously agreed meeting on the Kartarpur corridor on April 2 on the Pakistani side at Wagah.
Pakistan's Foreign Office spokesman alleged that Indian troops "intentionally targeted" civilians travelling in a civil bus on April 2 in Bagsar Sector.
Pakistan military today stated that Islamabad had the right to use any fighter jet in its 'legitimate self-defence' and it was immaterial whether an F-16 or a JF-17 shot down two Indian aircraft.
Pakistani UAV, F-16s spotted in Punjab's Khemkaran sector, forced to retreat after IAF scrambles jets
Tensions between India and Pakistan escalated after Indian Air Force fighter jets bombed terror group JeM's training camp near Balakot in Pakistan on February 26.
The kidnapping of the Hindu girls from Sindh is one of many cases of forced conversion and marriage of underage Hindu girls to Muslim men, common in villages close to the Indo-Pak border.
The next meeting on modalities would be scheduled only after India gets Pakistan's response over the indicated concerns, says MEA statement.