The development assumes significance as it comes on a day when at least 30 passengers on a Jet Airways flight from Mumbai to Jaipur suffered nose and ear bleeding after the crew "forgot" to turn on a switch that controls cabin air pressure.
The minister has also ordered a probe into the Jet Airways flight incident, which is being investigated by the Aircraft Accident Investigation Bureau (AAIB), an official statement said.
In recent times, there have been incidents of mid-air engine failures, involving the Pratt and Whitney (P&W) engine-powered Airbus A320 neo planes being operated by domestic budget carriers IndiGo and GoAir.
The minister has directed officials concerned to prepare a comprehensive safety audit plan, which involves assessment of safety parameters of all scheduled airlines, aerodromes, flying training schools and MROs (Maintenance, Repair and Overhaul Organisations) immediately, the statement said.
This comes weeks after the aviation regulator DGCA conducted a comprehensive financial audit of Air India and Jet Airways along with special safety audit of scheduled commuter airlines Air Deccan and Air Odisha.
"Minister has further directed that safety audit should be commenced forthwith and a report to this effect should be submitted for his perusal within 30 days," the statement added.
Last month, Prabhu asked the DGCA to submit a report on the status of these planes after IndiGo grounded five of its A320 neos due to non-availability of spare P&W engines.
At that time, he had asserted that the security of passengers is of paramount importance and it should not be compromised at any cost.
On the other hand, Jet Airways has reported as many as three incidents, including the one that took place Thursday, involving its pilots.
On August 6, the DGCA suspended flying licence of two of its pilots pending investigation after the commander attempted a take-off from a taxiway at Riyadh airport.
This resulted in the Boeing 737 aircraft, with 141 passengers on board, exceeding the the taxiway on to the unpaved area and ending up close to the exit of the taxiway.
On August 25, a Jet Airways Boeing 777 flight which was taxiing for take off for London from Delhi reportedly came to a sudden halt as the pilot did not have the ATC clearance.
Subsequently, both of its pilots were taken off from flying duties till investigations were completed.