He also said that the government has already asked all Indian airlines not to overfly Ukraine.
"It is unfortunate that this incident has happened. As far as our information... No Indians were on the flight. It is an unfortunate incident. No Indian citizen was on board," Raju told media persons in New Delhi.
All 298 people on board the Malaysian plane were killed on Thursday after the jet was shot down by "terrorists" over war-torn eastern Ukraine near the Russian border.
The minister said, "We have to be safe with our citizens...Our citizens are our concern. India has alerted its own airlines Jet or Air India and they are avoiding Ukraine as of now. We are happy with the information that we have got that no Indian citizen's life has been lost."
Aviation regulator, Director General of Civil Aviation had on Thursday issued instructions to Air India and Jet Airways, the only two Indian carriers that fly to Europe and North America, to avoid Ukrainian airspace while flying to and from destinations in both the continents.
An Air India official had said they would abide by any international advisory "to avoid airspace over conflict zone like Ukraine".
Ukraine airspace is among the busiest as flights connecting Europe and Asia transit through this region.
Malaysia Airlines flight shot down over Ukraine, 298 killed
IN PICS: The DEADLIEST air disasters in history
MH17 crash: Tears of disbelief hit relatives
Russia-backed militants shot down Malaysian aircraft
Tata-Singapore Airlines set to fly with new brand name