The ministry said since Captain Samant knew that the pilot assigned to operate the flight was grounded he should have arranged for alternative crew.
"The official had 24 hours to arrange for alternative crew but instead he allowed cancellation of the flight. I have asked the airline management to take him off roster pending an inquiry," said civil aviation minister Ajit Singh.
The minister added that he had asked the airline's chairman and managing director to transfer Captain Samant to another station.
Captain RS Dhillon who was to operate flight AI342 was suspended for fudging simulator entries.