A Qatar Airways plane from Doha and a Belgian aircraft from Hong Kong came within seconds of each other in the sky 148km west of Calcutta on Thursday.
The Qatar plane was headed to Calcutta while the TNT Airlines plane was going to Dubai. There were over 200 people on board the aircraft, which came dangerously close at 30,000ft in the air.
The air traffic control in Calcutta described the incident, around 12.30pm, as "a near miss".
The directorate general of civil aviation on Friday ordered a probe into the incident.
Airport sources said the Qatar Airways flight was at 35,000ft and the TNT flight at 30,000ft.
"The Qatar airways flight was asked to descend to one route but it descended to another because of a communication problem," said an airport official.
The pilots realised the planes were too close to each other when the in-flight pilot alarm system sounded an alert and asked the Qatar Airways flight to ascend.
A piece of equipment called TCAS (traffic collision avoidance system), which alerts the pilot if another aircraft is in the vicinity and provides guidance to avoid collision, is installed in most modern aircraft.
"We are probing the incident. The investigating official will submit a report," said an official of the directorate general of civil aviation.