A suspicious balloon-like object was reportedly spotted near New Delhi's Indira Gandhi International Airport on Wednesday.
On Tuesday, a similar suspicious object was shot down by an Indian Air Force fighter jet after it crossed over into Rajasthan from across the Pakistan border.
The defence ministry asked the external affairs ministry to take up the matter with Pakistan, Defence Minister Manohar Parrikar said at a press conference on Wednesday.
"Pakistan to be told to avoid such incidents in future. It seems Pakistan was testing our response," Parrikar said.
Earlier on Wednesday, two Nepal-bound flights from New Delhi were grounded after a threat call led to a bomb scare.
The deputy commissioner of police of the Airports received a Voice over Internet Protocol (VoIP) threat call which suggested a bomb threat to two Delhi-Kathmandu flights of Air India and Jet Airways. The flights were delayed and a bomb disposal squad conducted searches.
A similar bomb scare had grounded a flight from New Delhi on Monday as well.