"I think that is speculation .... There was no danger to our PM's aircraft. No problem. On Air Force One, the flight data is on foreign radar," Civil Aviation Minister Ashok Gajapathi Raju told reporters when asked whether there was any threat to the PM's plane which flew over the same airspace.
The prime minister returned on Thursday night after his trip to Brazil for the BRICS Summit.
"What happens is that whenever any air route (for a VIP aircraft) is finalised, the countries involved get to know about it. If you don't keep them informed, there is another type of problem," he said.
"So generally whenever any civilian aircraft flies over a country, suppose India, obviously the Government of India will know what aircraft it is, to whom it belongs, what its intentions are," Raju said.
All 298 people on board Malaysian Airlines plane were killed on Thursday after the jet was shot down by "terrorists" over war-torn eastern Ukraine near the Russian border.
Image: Prime Minister Modi boards the Air India One craft on his way to Brazil. Photograph. PTI
MH17 tragedy: Global outrage targets Russia, mourns the dead
6 passenger aircraft SHOT DOWN before MH17
MH17 crash: Tears of disbelief hit relatives
IN PICS: The DEADLIEST air disasters in history
In PHOTOS: Ukraine VS pro-Russian separatist fighters