Navtej Sarna, the Indian foreign ministry spokesman, told reporters in New Delhi: "A notice was sent a week before the test by Indian aviation authorities to ATC (air traffic control) Jakarta and other ATCs in the region informing them about the launch window dates, danger time, zone and height.
"The ATCs were requested to take action to issue notice to aviators and mariners in accordance with relevant ICAO (International Civil Aviation Organisation) provisions," Sarna said.
The statement came as Indonesia threatened to lodge a formal protest, with national carrier Garuda's operations director quoted as saying that "no prior information about the test" had been given.
The Boeing 747 jet carrying 400 people aborted its flight after 90 minutes and returned to the Indonesian capital Jakarta, an Indonesian report said.
Sarna also said India's missile tests were perfectly safe.
"India's missile testing programme has always followed the requisite safety precautions including in the case of the Agni missile test," he said.
The jet's exact location relative to the missile, which trailed orange and yellow smoke as it rocketed skyward, has not yet been made public.
Air India also said one of its incoming passenger flights from Singapore had to return to the city-state because of the missile launch, the Press Trust of India reported.
India announced on Thursday the successful test-firing of the medium-range ballistic missile, which can transport a one-tonne nuclear warhead as far away as Beijing.
The Agni-III (Fire-III) blasted off from Wheeler Island, 180 km northeast of Bhubaneswar, capital of the eastern Orissa state.